Variant report

Variant	rs706789
Chromosome Location	chr12:50459778-50459779
allele	A/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	MAX	chr12:50459710-50459825	NB4	blood:	n/a	chr12:50459751-50459761

No.	Distal block	Cell Line	Cell type
1	chr12:50449783..50453110-chr12:50454636..50460246,5	MCF-7	breast:
2	chr12:50459247..50461166-chr12:50463048..50465516,2	K562	blood:
3	chr12:50410767..50413288-chr12:50458291..50460266,2	K562	blood:
4	chr12:50417744..50420725-chr12:50458618..50461383,3	K562	blood:

Variant related genes	Relation type
ASIC1	TF binding region
ENSG00000110881	Chromatin interaction
ENSG00000161800	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs17124514	1.00[CEU][hapmap]
rs2307084	0.82[JPT][hapmap]
rs376184	0.80[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs386469	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs393848	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs404751	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs439171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs450423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs484951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4898546	0.80[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap]
rs590460	0.80[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs613066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627887	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs653576	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs685012	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs706794	0.80[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs835591	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835593	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835594	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836178	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs836184	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836185	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844359	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860699	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv437753	chr12:50454357-50462138	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50451400-50459800	Weak transcription	Fetal Heart	heart
2	chr12:50451400-50464000	Weak transcription	Fetal Lung	lung
3	chr12:50451800-50464200	Weak transcription	Gastric	stomach
4	chr12:50452000-50464200	Weak transcription	A549	lung
5	chr12:50452200-50464000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:50452400-50460200	Weak transcription	Hela-S3	cervix
7	chr12:50452600-50464000	Weak transcription	Esophagus	oesophagus
8	chr12:50453800-50460400	Strong transcription	Fetal Stomach	stomach
9	chr12:50454400-50460000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr12:50454600-50464200	Weak transcription	Fetal Intestine Small	intestine
11	chr12:50454800-50464000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:50455000-50459800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:50455600-50464200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:50455800-50464000	Weak transcription	Adipose Nuclei	Adipose
15	chr12:50456000-50460800	Enhancers	Fetal Muscle Leg	muscle
16	chr12:50456600-50463800	Weak transcription	Dnd41	blood
17	chr12:50456800-50460000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:50457200-50460000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:50457200-50460000	Weak transcription	NH-A	brain
20	chr12:50457400-50460000	Weak transcription	HSMM	muscle
21	chr12:50457400-50464000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:50458000-50461600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:50458200-50460200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
25	chr12:50458600-50459800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:50458600-50459800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:50458600-50459800	Weak transcription	Brain Angular Gyrus	brain
28	chr12:50458800-50459800	Weak transcription	HSMMtube	muscle
29	chr12:50458800-50463800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:50459000-50459800	Enhancers	Fetal Brain Male	brain
31	chr12:50459200-50460000	Enhancers	Brain Cingulate Gyrus	brain
32	chr12:50459200-50460200	Strong transcription	Primary T cells from cord blood	blood
33	chr12:50459200-50461200	Enhancers	Colon Smooth Muscle	Colon
34	chr12:50459400-50459800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:50459400-50460400	Genic enhancers	Fetal Muscle Trunk	muscle
36	chr12:50459400-50460600	Enhancers	Brain Anterior Caudate	brain
37	chr12:50459400-50460600	Genic enhancers	Brain Substantia Nigra	brain
38	chr12:50459400-50460800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:50459400-50460800	Strong transcription	Brain Germinal Matrix	brain
40	chr12:50459400-50461000	Enhancers	NHDF-Ad	bronchial
41	chr12:50459400-50461600	Weak transcription	Fetal Brain Female	brain
42	chr12:50459600-50459800	Enhancers	Fetal Thymus	thymus
43	chr12:50459600-50460200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:50459600-50460400	Enhancers	Right Atrium	heart
45	chr12:50459600-50460600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:50459600-50460600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:50459600-50460600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:50459600-50460600	Enhancers	Psoas Muscle	Psoas
49	chr12:50459600-50460600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr12:50459600-50460800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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