Variant report

Variant	rs6489475
Chromosome Location	chr12:495558-495559
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:495552-495677	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:494061..497561-chr12:499622..502914,3	K562	blood:
2	chr12:490753..496037-chr12:496468..499221,8	MCF-7	breast:

Variant related genes	Relation type
CCDC77	TF binding region
ENSG00000120647	Chromatin interaction
ENSG00000073614	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1011699	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10744616	0.87[AMR][1000 genomes]
rs10774150	0.87[AMR][1000 genomes]
rs10774154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1155942	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11608938	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17800744	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1860360	0.91[AMR][1000 genomes]
rs2041299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098094	0.83[AMR][1000 genomes]
rs2159364	0.91[AMR][1000 genomes]
rs2253565	0.92[AMR][1000 genomes]
rs507597	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61907026	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61907030	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61907031	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6489450	0.84[AMR][1000 genomes]
rs6489452	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7133796	0.82[AMR][1000 genomes]
rs7135768	0.81[AMR][1000 genomes]
rs7311496	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965038	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977462	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6489475	CCDC77	cis	Artery Tibial	GTEx
rs6489475	JARID1A	Cis_1M	lymphoblastoid	RTeQTL
rs6489475	CCDC77	cis	Thyroid	GTEx
rs6489475	KDM5A	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:475200-496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:485400-495600	Weak transcription	Psoas Muscle	Psoas
3	chr12:486000-497200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:486400-497200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:487000-496200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:488000-496600	Weak transcription	Right Ventricle	heart
7	chr12:488200-495600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:492000-495600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:492800-497000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:493400-495600	Genic enhancers	Dnd41	blood
11	chr12:493400-496800	Weak transcription	Colonic Mucosa	Colon
12	chr12:493600-495600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:493600-495600	Weak transcription	Ovary	ovary
14	chr12:493600-495600	Weak transcription	Right Atrium	heart
15	chr12:493600-496200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:493600-496800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:493600-496800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:493600-496800	Weak transcription	Aorta	Aorta
19	chr12:493600-497000	Weak transcription	Lung	lung
20	chr12:493600-497200	Weak transcription	Gastric	stomach
21	chr12:493800-495800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:494000-495600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:494000-495600	Weak transcription	Placenta	Placenta
24	chr12:494000-495800	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr12:494000-496200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:494000-496600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr12:494200-495600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:494200-495600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:494200-495600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:494200-495600	Weak transcription	K562	blood
31	chr12:494200-495800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:494200-496200	Weak transcription	Fetal Intestine Large	intestine
33	chr12:494200-496600	Weak transcription	Fetal Stomach	stomach
34	chr12:494200-496800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr12:494200-497000	Weak transcription	Esophagus	oesophagus
36	chr12:494200-497200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:494400-495600	Weak transcription	Fetal Intestine Small	intestine
38	chr12:494600-496600	Enhancers	Adipose Nuclei	Adipose
39	chr12:494800-495600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:494800-495600	Genic enhancers	Primary B cells from cord blood	blood
41	chr12:494800-495600	Enhancers	Primary T cells from cord blood	blood
42	chr12:494800-495600	Genic enhancers	Primary hematopoietic stem cells	blood
43	chr12:494800-495600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr12:494800-495600	Genic enhancers	Fetal Lung	lung
45	chr12:494800-495600	Genic enhancers	Rectal Mucosa Donor 31	rectum
46	chr12:494800-495600	Enhancers	HepG2	liver
47	chr12:494800-495800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:494800-495800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr12:494800-495800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:494800-495800	Enhancers	Cortex derived primary cultured neurospheres	brain

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