Variant report

Variant	rs7312134
Chromosome Location	chr12:59990748-59990749
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	POLR2A	chr12:59989388-59991554	GM12892	blood:	n/a	n/a
2	CTCF	chr12:59990720-59990870	GM12872	blood:	n/a	n/a
3	MYC	chr12:59989184-59991670	NB4	blood:	n/a	chr12:59990810-59990825
4	CTCF	chr12:59990640-59990790	GM12864	blood:	n/a	n/a
5	CTCF	chr12:59990720-59990870	GM12875	blood:	n/a	n/a
6	CTCF	chr12:59990700-59990850	GM12873	blood:	n/a	n/a
7	CTCF	chr12:59990714-59990856	Gliobla	brain:	n/a	n/a
8	ELF1	chr12:59990484-59991120	MCF-7	breast:	n/a	chr12:59991059-59991070
9	POLR2A	chr12:59989734-59991087	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr12:59989531-59991141	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:59989341-59991607	Raji	blood:	n/a	n/a
12	POLR2A	chr12:59989748-59991058	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr12:59990696-59990929	MCF-7	breast:	n/a	n/a
14	CHD2	chr12:59989937-59991017	H1-hESC	embryonic stem cell:	n/a	n/a
15	ETS1	chr12:59990189-59990876	GM12878	blood:	n/a	chr12:59990502-59990513 chr12:59990558-59990569
16	POLR2A	chr12:59989314-59991660	GM12878	blood:	n/a	n/a
17	CTCF	chr12:59990680-59990830	GM12865	blood:	n/a	n/a
18	CTCF	chr12:59990640-59990790	GM12874	blood:	n/a	n/a
19	ELK1	chr12:59990342-59991537	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr12:59990660-59990810	GM06990	blood:	n/a	n/a
21	MAZ	chr12:59989015-59992085	IMR90	lung:	n/a	chr12:59990810-59990825
22	CTCF	chr12:59990668-59990948	MCF-7	breast:	n/a	n/a
23	POLR2A	chr12:59989257-59991805	GM12891	blood:	n/a	n/a
24	YY1	chr12:59990287-59990981	GM12892	blood:	n/a	chr12:59990627-59990646
25	POU2F2	chr12:59990639-59990981	GM12891	blood:	n/a	n/a
26	CTCF	chr12:59990720-59990881	A549	lung:	n/a	n/a
27	MAX	chr12:59989500-59991421	GM12878	blood:	n/a	chr12:59990810-59990825
28	CTCF	chr12:59990696-59990933	GM19239	blood:	n/a	n/a
29	TAF1	chr12:59990693-59991020	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr12:59989367-59991683	GM19193	blood:	n/a	n/a
31	MAX	chr12:59989757-59991112	H1-hESC	embryonic stem cell:	n/a	chr12:59990810-59990825
32	CTCF	chr12:59990740-59990890	Hela-S3	cervix:	n/a	n/a
33	STAT1	chr12:59989489-59991608	Hela-S3	cervix:	n/a	chr12:59989845-59989857
34	POLR2A	chr12:59989730-59991574	GM12878	blood:	n/a	n/a
35	ATF2	chr12:59990321-59991736	GM12878	blood:	n/a	n/a
36	USF1	chr12:59990597-59991051	H1-hESC	embryonic stem cell:	n/a	chr12:59990812-59990825 chr12:59990783-59990794
37	SPI1	chr12:59990417-59991329	HL-60	blood:	n/a	chr12:59990559-59990572
38	TCF12	chr12:59990650-59990911	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr12:59989458-59991600	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr12:59990609-59990956	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr12:59989339-59991769	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr12:59989934-59991033	GM12892	blood:	n/a	n/a
43	CREB1	chr12:59989775-59991005	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr12:59990680-59990830	AG10803	skin:	n/a	n/a
45	POLR2A	chr12:59990609-59990941	GM12891	blood:	n/a	n/a
46	POLR2A	chr12:59989354-59991625	HL-60	blood:	n/a	n/a
47	MAX	chr12:59989820-59991020	MCF-7	breast:	n/a	chr12:59990810-59990825
48	POLR2A	chr12:59989388-59991638	GM18505	blood:	n/a	n/a
49	MAX	chr12:59989619-59991107	H1-hESC	embryonic stem cell:	n/a	chr12:59990810-59990825
50	CTCF	chr12:59990720-59990870	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59990404..59991079-chr15:65596908..65597443,2	Hela-S3	cervix:

Variant related genes	Relation type
SLC16A7	TF binding region
ENSG00000200156	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10506395	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732745	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735880	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735881	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747847	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10747848	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10747850	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747851	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747852	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783988	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10783989	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10783992	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877315	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877320	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173084	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11173085	0.84[EUR][1000 genomes]
rs11173087	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11173090	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391130	0.90[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497470	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566164	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1908977	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1966281	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2132871	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2132873	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2646311	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2671854	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3106580	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35986083	0.88[EUR][1000 genomes]
rs4019983	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420644	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs4421780	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4536269	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635118	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4760291	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4760292	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760293	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760294	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581255	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6581256	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6581257	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581258	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581259	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581260	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581261	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133515	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133612	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303302	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970605	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975216	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974459	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1048949	chr12:59974039-60041477	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1038100	chr12:59983391-60018745	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59988800-59991000	Active TSS	Thymus	Thymus
2	chr12:59988800-59991600	Active TSS	Duodenum Mucosa	Duodenum
3	chr12:59988800-59991800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:59989000-59990800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:59989000-59991000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:59989000-59991000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:59989000-59991000	Active TSS	Fetal Brain Female	brain
8	chr12:59989000-59991000	Active TSS	Fetal Thymus	thymus
9	chr12:59989000-59991000	Active TSS	NHLF	lung
10	chr12:59989000-59991400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr12:59989000-59991400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:59989000-59991400	Active TSS	Right Ventricle	heart
13	chr12:59989000-59991600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:59989000-59991600	Active TSS	Brain Germinal Matrix	brain
15	chr12:59989000-59991600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr12:59989000-59992000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr12:59989200-59990800	Active TSS	Fetal Muscle Leg	muscle
18	chr12:59989200-59991000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr12:59989200-59991000	Active TSS	Primary B cells from peripheral blood	blood
20	chr12:59989200-59991000	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr12:59989200-59991000	Active TSS	Brain Anterior Caudate	brain
22	chr12:59989200-59991000	Active TSS	Fetal Intestine Large	intestine
23	chr12:59989200-59991200	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr12:59989200-59991200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:59989200-59991200	Active TSS	Brain Angular Gyrus	brain
26	chr12:59989200-59991200	Active TSS	Brain Cingulate Gyrus	brain
27	chr12:59989200-59991200	Active TSS	Brain Substantia Nigra	brain
28	chr12:59989200-59991200	Active TSS	Colon Smooth Muscle	Colon
29	chr12:59989200-59991200	Active TSS	Hela-S3	cervix
30	chr12:59989200-59991200	Active TSS	HSMMtube	muscle
31	chr12:59989200-59991400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:59989200-59991400	Active TSS	Fetal Muscle Trunk	muscle
33	chr12:59989200-59991400	Active TSS	Psoas Muscle	Psoas
34	chr12:59989200-59991400	Bivalent/Poised TSS	A549	lung
35	chr12:59989200-59991600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:59989200-59991600	Active TSS	GM12878-XiMat	blood
37	chr12:59989200-59991800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:59989200-59991800	Active TSS	NHDF-Ad	bronchial
39	chr12:59989200-59992000	Active TSS	Aorta	Aorta
40	chr12:59989200-59992000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:59989200-59992000	Active TSS	Right Atrium	heart
42	chr12:59989400-59990800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:59989400-59990800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:59989400-59990800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:59989400-59990800	Active TSS	Fetal Heart	heart
46	chr12:59989400-59991000	Active TSS	H9 Cell Line	embryonic stem cell
47	chr12:59989400-59991000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:59989400-59991000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr12:59989400-59991000	Active TSS	Lung	lung
50	chr12:59989400-59991000	Active TSS	Sigmoid Colon	Sigmoid Colon

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