Variant report

Variant	rs12239437
Chromosome Location	chr1:158975557-158975558
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	chr1:158975396-158975649	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF7L2	chr1:158975519-158977197	HEK293	kidney:	n/a	chr1:158976924-158976940 chr1:158976924-158976940 chr1:158976925-158976939 chr1:158976926-158976936 chr1:158976927-158976936
3	SIN3AK20	chr1:158975388-158975862	PFSK-1	brain:	n/a	n/a
4	CTCF	chr1:158975480-158975630	GM12869	blood:	n/a	n/a
5	KAP1	chr1:158974765-158977041	U2OS	brain:	n/a	chr1:158975441-158975449
6	STAT3	chr1:158975308-158975720	MCF10A-Er-Src	breast:	n/a	chr1:158975477-158975500 chr1:158975572-158975583 chr1:158975573-158975582 chr1:158975574-158975583 chr1:158975490-158975501 chr1:158975492-158975500
7	FOXP2	chr1:158975447-158975777	SK-N-MC	brain:	n/a	n/a
8	TAF1	chr1:158975146-158975988	PFSK-1	brain:	n/a	n/a
9	KAP1	chr1:158974927-158976564	HEK293	kidney:	n/a	chr1:158975441-158975449
10	POLR2A	chr1:158974970-158976279	PFSK-1	brain:	n/a	n/a
11	CTCF	chr1:158975480-158975630	HPAF	blood vessel:	n/a	n/a
12	FOXP2	chr1:158975391-158975857	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr1:158975192-158976071	PFSK-1	brain:	n/a	n/a
14	EP300	chr1:158975328-158975839	SK-N-SH_RA	brain:	n/a	chr1:158975642-158975651
15	EP300	chr1:158975329-158975783	SK-N-SH_RA	brain:	n/a	chr1:158975642-158975651
16	REST	chr1:158975315-158975838	PFSK-1	brain:	n/a	chr1:158975777-158975790
17	STAT3	chr1:158975519-158975600	MCF10A-Er-Src	breast:	n/a	chr1:158975572-158975583 chr1:158975573-158975582 chr1:158975574-158975583
18	CUX1	chr1:158975551-158975617	GM12878	blood:	n/a	n/a
19	FOS	chr1:158975437-158975650	MCF10A-Er-Src	breast:	n/a	n/a
20	SIN3AK20	chr1:158975397-158975862	PFSK-1	brain:	n/a	n/a
21	REST	chr1:158975353-158975876	PFSK-1	brain:	n/a	chr1:158975777-158975790
22	STAT3	chr1:158975106-158975805	MCF10A-Er-Src	breast:	n/a	chr1:158975477-158975500 chr1:158975572-158975583 chr1:158975573-158975582 chr1:158975574-158975583 chr1:158975490-158975501 chr1:158975492-158975500
23	TEAD4	chr1:158975426-158975809	K562	blood:	n/a	n/a
24	STAT3	chr1:158975112-158975744	MCF10A-Er-Src	breast:	n/a	chr1:158975477-158975500 chr1:158975572-158975583 chr1:158975573-158975582 chr1:158975574-158975583 chr1:158975490-158975501 chr1:158975492-158975500
25	FOS	chr1:158975438-158975637	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1102013	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1102014	0.96[ASN][1000 genomes]
rs1102015	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1102016	0.81[ASN][1000 genomes]
rs11590737	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.93[ASN][1000 genomes]
rs1578477	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1614568	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs1615480	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1623601	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs1772443	0.94[ASN][1000 genomes]
rs1935068	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1935070	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1935071	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276404	0.83[JPT][hapmap]
rs2793856	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793857	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754464	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3754466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41264051	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56954127	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57218670	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57498847	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58506115	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58805430	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60086314	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60381726	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61254442	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71632651	0.98[ASN][1000 genomes]
rs72480244	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72480246	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72480247	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72480248	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856064	0.83[JPT][hapmap]
rs856125	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs856126	0.97[ASN][1000 genomes]
rs856127	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs856131	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs856132	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs856133	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856134	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856135	0.81[ASN][1000 genomes]
rs856136	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856140	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs856141	0.81[ASN][1000 genomes]
rs856142	0.81[ASN][1000 genomes]
rs860635	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158968600-158977400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:158968800-158977000	Weak transcription	Primary T cells from cord blood	blood
3	chr1:158969000-158977200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:158969000-158977400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:158969000-158978200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:158970000-158978600	Weak transcription	Esophagus	oesophagus
7	chr1:158970200-158978600	Weak transcription	Psoas Muscle	Psoas
8	chr1:158970200-158978800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:158970200-158979200	Weak transcription	Aorta	Aorta
10	chr1:158970800-158980800	Weak transcription	Pancreas	Pancrea
11	chr1:158971000-158978400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:158971200-158978400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:158971200-158978400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:158971200-158978400	Weak transcription	HSMM	muscle
15	chr1:158971200-158978600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:158971200-158978600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:158971200-158978800	Weak transcription	HSMMtube	muscle
18	chr1:158971400-158978400	Weak transcription	Hela-S3	cervix
19	chr1:158971800-158978600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:158971800-158979800	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:158972000-158979600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:158974400-158976000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:158974800-158975600	Enhancers	Adipose Nuclei	Adipose
24	chr1:158974800-158975600	Enhancers	Fetal Muscle Leg	muscle
25	chr1:158974800-158975600	Enhancers	Left Ventricle	heart
26	chr1:158974800-158975600	Enhancers	Ovary	ovary
27	chr1:158974800-158975800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:158974800-158975800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:158974800-158975800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr1:158974800-158975800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:158974800-158975800	Enhancers	Fetal Intestine Large	intestine
32	chr1:158974800-158975800	Enhancers	Placenta	Placenta
33	chr1:158974800-158975800	Enhancers	Osteobl	bone
34	chr1:158974800-158976000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:158974800-158976000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:158974800-158976000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:158974800-158976000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:158974800-158976200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:158974800-158976400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:158974800-158977600	Enhancers	Small Intestine	intestine
41	chr1:158974800-158977800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:158974800-158978400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:158975000-158975600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
44	chr1:158975000-158975600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:158975000-158975600	Enhancers	Brain Anterior Caudate	brain
46	chr1:158975000-158975600	Enhancers	NHLF	lung
47	chr1:158975000-158975800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:158975000-158976000	Enhancers	Fetal Stomach	stomach
49	chr1:158975000-158977600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:158975000-158978800	Enhancers	Primary B cells from peripheral blood	blood

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