Variant report

Variant	rs4963948
Chromosome Location	chr12:26145382-26145383
allele	G/T
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	FOS	chr12:26145364-26145606	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr12:26145280-26145649	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr12:26145280-26145609	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr12:26145052-26145505	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr12:26145346-26145627	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr12:26145361-26145527	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
RASSF8	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10219479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11048395	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11048396	0.91[CEU][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12300961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12304275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12308128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16929960	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17354107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17354204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17354478	0.91[CEU][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17361182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361755	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17362314	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17362453	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17362593	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17362614	0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17362901	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17458637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17459432	0.91[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17459771	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17459910	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17460800	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1996091	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4963645	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4963944	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs4963945	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4963949	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4963950	0.84[ASN][1000 genomes]
rs55965624	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56051193	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56169892	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56228589	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56369291	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56399330	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58178281	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73074880	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73074882	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73074895	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73077109	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73077123	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73077138	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077155	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73077158	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73079015	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73079022	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73079027	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73079032	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73079036	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73079055	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73079059	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7486150	1.00[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758300	chr12:25992331-26161116	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759886	chr12:25992331-26161116	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv522351	chr12:26127230-26149703	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv983482	chr12:26142257-26146356	Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26117600-26150000	Weak transcription	Hela-S3	cervix
2	chr12:26131000-26145400	Weak transcription	Lung	lung
3	chr12:26131000-26146000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:26131000-26146200	Weak transcription	HSMM	muscle
5	chr12:26132400-26146800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:26134200-26148000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:26134400-26145400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:26134400-26145400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:26134400-26147800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:26138400-26146800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:26138800-26145400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:26139200-26147400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:26139400-26146000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:26139400-26150600	Weak transcription	Brain Angular Gyrus	brain
15	chr12:26139600-26145800	Weak transcription	Brain Substantia Nigra	brain
16	chr12:26139600-26160000	Weak transcription	Pancreas	Pancrea
17	chr12:26139800-26146800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:26140200-26145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:26140200-26145600	Weak transcription	Aorta	Aorta
20	chr12:26140200-26147600	Weak transcription	Ovary	ovary
21	chr12:26141800-26146800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:26142000-26149000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:26142200-26145400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:26142200-26145600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:26142200-26145600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:26142200-26146400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:26142200-26146400	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:26142200-26146400	Weak transcription	Fetal Stomach	stomach
29	chr12:26142200-26155600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:26142400-26145400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:26142800-26145400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:26142800-26145400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:26143800-26147400	Enhancers	Brain Anterior Caudate	brain
34	chr12:26143800-26151200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr12:26143800-26151200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr12:26144000-26151200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr12:26144000-26151600	Enhancers	Colon Smooth Muscle	Colon
38	chr12:26144400-26145400	Enhancers	HUVEC	blood vessel
39	chr12:26144400-26145800	Enhancers	Right Atrium	heart
40	chr12:26144400-26146000	Enhancers	Right Ventricle	heart
41	chr12:26144400-26146200	Enhancers	Left Ventricle	heart
42	chr12:26144400-26146600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:26144400-26148000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr12:26144400-26148200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:26144400-26152200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr12:26144600-26145600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:26144600-26145800	Enhancers	Psoas Muscle	Psoas
48	chr12:26144600-26146000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:26144600-26146000	Enhancers	NHEK	skin
50	chr12:26144600-26146600	Enhancers	HMEC	breast

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