Variant report

Variant	rs2601650
Chromosome Location	chr1:215178745-215178746
allele	A/C/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	GATA3	chr1:215178405-215178806	T-47D	breast:	n/a	chr1:215178573-215178581 chr1:215178424-215178445 chr1:215178663-215178671 chr1:215178431-215178438 chr1:215178567-215178588 chr1:215178519-215178526 chr1:215178431-215178438 chr1:215178564-215178571 chr1:215178430-215178440 chr1:215178431-215178438 chr1:215178563-215178571
2	MAX	chr1:215178409-215178910	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr1:215177759-215178931	SK-N-SH	brain:	n/a	chr1:215178595-215178611
4	JUND	chr1:215177531-215179055	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr1:215177263-215179503	SK-N-SH	brain:	n/a	chr1:215178595-215178611
6	EP300	chr1:215177121-215179036	SK-N-SH	brain:	n/a	chr1:215177436-215177443 chr1:215177155-215177169
7	GATA3	chr1:215176919-215179889	SK-N-SH	brain:	n/a	chr1:215178573-215178581 chr1:215177232-215177239 chr1:215178424-215178445 chr1:215177231-215177241 chr1:215178663-215178671 chr1:215177228-215177244 chr1:215177232-215177241 chr1:215177225-215177246 chr1:215178431-215178438 chr1:215178567-215178588 chr1:215178519-215178526 chr1:215178431-215178438 chr1:215178564-215178571 chr1:215178430-215178440 chr1:215178431-215178438 chr1:215178563-215178571
8	GATA3	chr1:215177564-215178912	SH-SY5Y	brain:	n/a	chr1:215178573-215178581 chr1:215178424-215178445 chr1:215178663-215178671 chr1:215178431-215178438 chr1:215178567-215178588 chr1:215178519-215178526 chr1:215178431-215178438 chr1:215178564-215178571 chr1:215178430-215178440 chr1:215178431-215178438 chr1:215178563-215178571
9	POLR2A	chr1:215178583-215179437	ProgFib	skin:	n/a	n/a
10	GATA3	chr1:215178100-215179023	MCF-7	breast:	n/a	chr1:215178573-215178581 chr1:215178424-215178445 chr1:215178663-215178671 chr1:215178431-215178438 chr1:215178567-215178588 chr1:215178519-215178526 chr1:215178431-215178438 chr1:215178564-215178571 chr1:215178430-215178440 chr1:215178431-215178438 chr1:215178563-215178571
11	TEAD4	chr1:215177551-215179251	SK-N-SH	brain:	n/a	n/a
12	FOXM1	chr1:215177680-215178918	SK-N-SH	brain:	n/a	n/a
13	PBX3	chr1:215176971-215179297	SK-N-SH	brain:	n/a	n/a
14	KAP1	chr1:215177693-215179237	HEK293	kidney:	n/a	n/a
15	POLR2A	chr1:215178442-215178796	SK-N-SH	brain:	n/a	n/a
16	TCF12	chr1:215177258-215179099	SK-N-SH	brain:	n/a	n/a
17	TAF1	chr1:215178556-215178748	SK-N-SH	brain:	n/a	n/a
18	RAD21	chr1:215178442-215178844	SK-N-SH_RA	brain:	n/a	n/a
19	TCF7L2	chr1:215177885-215179318	HEK293	kidney:	n/a	chr1:215179223-215179237 chr1:215178766-215178775 chr1:215179222-215179238 chr1:215179222-215179238
20	MAX	chr1:215178424-215179370	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr1:215177461-215179302	SK-N-SH	brain:	n/a	n/a
22	EP300	chr1:215178374-215178852	SK-N-SH_RA	brain:	n/a	n/a
23	GATA3	chr1:215178223-215178917	MCF-7	breast:	n/a	chr1:215178573-215178581 chr1:215178424-215178445 chr1:215178663-215178671 chr1:215178431-215178438 chr1:215178567-215178588 chr1:215178519-215178526 chr1:215178431-215178438 chr1:215178564-215178571 chr1:215178430-215178440 chr1:215178431-215178438 chr1:215178563-215178571
24	FOXM1	chr1:215177607-215179327	SK-N-SH	brain:	n/a	n/a
25	YY1	chr1:215178455-215178838	SK-N-SH	brain:	n/a	n/a
26	MEF2A	chr1:215178251-215178929	SK-N-SH	brain:	n/a	chr1:215178702-215178717 chr1:215178704-215178715
27	PBX3	chr1:215177125-215178912	SK-N-SH	brain:	n/a	n/a
28	GATA3	chr1:215176924-215179719	SK-N-SH	brain:	n/a	chr1:215178573-215178581 chr1:215177232-215177239 chr1:215178424-215178445 chr1:215177231-215177241 chr1:215178663-215178671 chr1:215177228-215177244 chr1:215177232-215177241 chr1:215177225-215177246 chr1:215178431-215178438 chr1:215178567-215178588 chr1:215178519-215178526 chr1:215178431-215178438 chr1:215178564-215178571 chr1:215178430-215178440 chr1:215178431-215178438 chr1:215178563-215178571
29	EP300	chr1:215177501-215179088	SK-N-SH	brain:	n/a	n/a
30	FOSL2	chr1:215177680-215179205	SK-N-SH	brain:	n/a	n/a
31	JUND	chr1:215177410-215178959	SK-N-SH	brain:	n/a	n/a
32	GATA2	chr1:215176679-215179272	SH-SY5Y	brain:	n/a	chr1:215177232-215177239 chr1:215178424-215178445 chr1:215177231-215177241 chr1:215178663-215178671 chr1:215177228-215177244 chr1:215177232-215177241 chr1:215177225-215177246 chr1:215178431-215178438 chr1:215178567-215178588 chr1:215178519-215178526 chr1:215178431-215178438 chr1:215178564-215178571 chr1:215178430-215178440 chr1:215178431-215178438
33	KAP1	chr1:215178121-215178960	U2OS	brain:	n/a	n/a
34	EP300	chr1:215177056-215178799	SK-N-SH_RA	brain:	n/a	chr1:215177436-215177443 chr1:215177155-215177169
35	TEAD4	chr1:215177601-215179003	SK-N-SH	brain:	n/a	n/a
36	TCF12	chr1:215177195-215179578	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
KCNK2	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10494989	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10494991	0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10494992	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10779633	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10779634	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10779635	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12026832	0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12141327	0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1377173	0.84[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1377175	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1377177	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1452608	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1452609	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1452610	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1545504	0.86[ASN][1000 genomes]
rs1584759	0.98[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1584760	0.81[ASN][1000 genomes]
rs1597847	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17024148	0.93[CHD][hapmap]
rs1869201	0.83[ASN][1000 genomes]
rs2123331	0.93[CHD][hapmap]
rs2262937	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601607	0.81[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601609	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2601610	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601611	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601612	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601613	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2601614	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601615	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601616	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601617	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601618	0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601619	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601620	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601621	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601622	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601623	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601624	0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601625	0.85[CEU][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs2601634	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2601636	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601638	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601639	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601640	0.85[CEU][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601641	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2601646	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2802642	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2802643	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2802644	0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2802649	0.84[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2802650	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2802651	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2802657	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2841574	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2841575	0.98[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs2841577	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2841581	0.88[ASN][1000 genomes]
rs2841587	0.88[ASN][1000 genomes]
rs2841591	0.89[ASN][1000 genomes]
rs2841592	0.89[ASN][1000 genomes]
rs2841595	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2841596	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841597	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841598	0.85[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841599	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841600	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841601	0.90[ASN][1000 genomes]
rs2841602	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841604	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841605	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841606	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841607	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841608	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841609	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841610	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841611	0.85[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2841612	0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841613	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2841615	0.98[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2841616	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2841621	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2841622	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4294386	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4339836	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4348692	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4356023	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61820010	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468105	chr1:215167236-215248417	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv549182	chr1:215167236-215248417	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2601650	ESRRG	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215176000-215178800	Weak transcription	HSMMtube	muscle
2	chr1:215177200-215178800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:215177200-215211200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:215177400-215179400	Enhancers	Fetal Muscle Leg	muscle
5	chr1:215177600-215179200	Enhancers	NHLF	lung
6	chr1:215177800-215178800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:215178200-215178800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:215178200-215178800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:215178400-215179400	Enhancers	NH-A	brain
10	chr1:215178600-215178800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:215178600-215178800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:215178600-215178800	Flanking Active TSS	NHDF-Ad	bronchial
13	chr1:215178600-215178800	Enhancers	NHEK	skin
14	chr1:215178600-215179000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:215178600-215179200	Enhancers	HSMM	muscle
16	chr1:215178600-215179200	Flanking Active TSS	Osteobl	bone
17	chr1:215178600-215179400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:215178600-215179600	Enhancers	Adipose Nuclei	Adipose
19	chr1:215178600-215179600	Enhancers	Fetal Lung	lung
20	chr1:215178600-215179800	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr1:215178600-215180000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:215178600-215180000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:215178600-215181000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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