Variant report

Variant	rs16930401
Chromosome Location	chr12:511457-511458
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:497611..500419-chr12:508788..511712,2	MCF-7	breast:
2	chr12:496401..500895-chr12:509695..513736,6	K562	blood:

Variant related genes	Relation type
ENSG00000120647	Chromatin interaction
ENSG00000073614	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1017162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs11062187	1.00[CEU][hapmap]
rs11062328	1.00[EUR][1000 genomes]
rs11062353	1.00[EUR][1000 genomes]
rs11062355	1.00[EUR][1000 genomes]
rs11062465	1.00[EUR][1000 genomes]
rs11062616	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11062659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11062769	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12298836	1.00[EUR][1000 genomes]
rs12303118	1.00[EUR][1000 genomes]
rs12303378	1.00[EUR][1000 genomes]
rs12304242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12306188	0.82[EUR][1000 genomes]
rs12314514	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12315694	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12317905	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12321487	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12321513	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12321532	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12321546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1541584	1.00[EUR][1000 genomes]
rs16929851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2267987	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2284335	1.00[EUR][1000 genomes]
rs2284336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2300128	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2300130	0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs2305164	1.00[CEU][hapmap]
rs2887438	0.95[AMR][1000 genomes]
rs3753160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759370	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3803158	0.95[AMR][1000 genomes]
rs3803159	0.95[AMR][1000 genomes]
rs3815557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs4980816	0.90[AMR][1000 genomes]
rs4980873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4980887	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4980893	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57580513	0.90[EUR][1000 genomes]
rs58979246	1.00[EUR][1000 genomes]
rs720127	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs7487555	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7488483	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7954487	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7970562	1.00[EUR][1000 genomes]
rs9804967	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051726	chr12:282465-511843	Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541304	chr12:282465-635505	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1042991	chr12:282465-666255	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1041574	chr12:282465-812000	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv1050781	chr12:321353-783899	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv1040849	chr12:321619-771493	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv541322	chr12:321619-771493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv1035679	chr12:321619-781558	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv1053519	chr12:321619-828175	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
14	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
15	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
16	esv2757484	chr12:335010-543206	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
18	nsv1045638	chr12:349031-893536	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
19	nsv541325	chr12:349031-893536	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
20	nsv1050646	chr12:362398-658665	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
21	nsv541326	chr12:362398-658665	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
22	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
23	nsv898565	chr12:428131-564185	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
24	nsv1052201	chr12:429128-515675	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
25	nsv541328	chr12:429128-515675	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
26	nsv442250	chr12:432808-543847	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	esv2756520	chr12:433151-543206	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
28	nsv1050226	chr12:441032-743195	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
29	nsv1035222	chr12:449993-515675	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
30	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
31	nsv949226	chr12:493900-814882	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
32	nsv898566	chr12:499041-570917	Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
33	nsv1036822	chr12:504573-586674	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
34	nsv541329	chr12:504573-586674	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
35	nsv514668	chr12:506474-521532	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:509400-511800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:510000-511600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:510000-511600	Active TSS	Fetal Intestine Small	intestine
4	chr12:510000-511800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:510000-511800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr12:510000-511800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:510000-511800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:510000-512000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr12:510000-512000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:510000-512000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:510000-512000	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr12:510000-512000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:510000-512200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:510000-512200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr12:510000-512200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:510200-511600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr12:510200-511600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:510200-511600	Active TSS	Fetal Brain Female	brain
19	chr12:510200-511600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr12:510200-511600	Active TSS	Right Atrium	heart
21	chr12:510200-511600	Active TSS	HSMM	muscle
22	chr12:510200-511600	Active TSS	HSMMtube	muscle
23	chr12:510200-511600	Active TSS	K562	blood
24	chr12:510200-511600	Active TSS	NHDF-Ad	bronchial
25	chr12:510200-511800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:510200-512000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr12:510200-512000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:510200-512000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:510200-512000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:510400-511600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:510400-511600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:510400-511600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:510400-511600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:510400-511600	Active TSS	Esophagus	oesophagus
35	chr12:510400-511600	Active TSS	Fetal Heart	heart
36	chr12:510400-511600	Active TSS	Fetal Muscle Trunk	muscle
37	chr12:510400-511600	Active TSS	Placenta	Placenta
38	chr12:510400-511600	Active TSS	A549	lung
39	chr12:510400-511600	Active TSS	Hela-S3	cervix
40	chr12:510400-511600	Bivalent/Poised TSS	HepG2	liver
41	chr12:510400-511800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:510400-511800	Active TSS	Colonic Mucosa	Colon
43	chr12:510400-511800	Active TSS	NHLF	lung
44	chr12:510400-512000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:510400-512000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr12:510400-512000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:510400-512400	Active TSS	GM12878-XiMat	blood
48	chr12:510600-511600	Active TSS	Dnd41	blood
49	chr12:510600-511600	Active TSS	HMEC	breast
50	chr12:510600-511600	Active TSS	NH-A	brain

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