Variant report

Variant	rs6656858
Chromosome Location	chr1:197113573-197113574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:193072582..193075085-chr1:197113385..197115206,2	K562	blood:
2	chr1:197110180..197113762-chr1:197163844..197167381,3	K562	blood:
3	chr1:197112577..197117711-chr1:197168565..197172597,7	K562	blood:
4	chr1:197092500..197094237-chr1:197110834..197113696,2	K562	blood:
5	chr1:197100050..197103962-chr1:197110434..197115621,7	K562	blood:
6	chr1:197112577..197117470-chr1:197168821..197172597,7	K562	blood:

Variant related genes	Relation type
ENSG00000177888	Chromatin interaction
ENSG00000023572	Chromatin interaction
ENSG00000134376	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1034162	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10429911	0.87[CEU][hapmap]
rs10732295	0.87[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs10732296	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs10733087	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10737687	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10754213	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10754214	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10754215	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10754219	0.87[CEU][hapmap]
rs10801587	0.90[EUR][1000 genomes]
rs10801588	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10801590	0.90[EUR][1000 genomes]
rs10801591	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10922165	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10922166	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10922169	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1115246	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1115247	1.00[CEU][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1170880	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs1170881	1.00[CEU][hapmap]
rs12039586	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12092294	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs12677	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12731209	1.00[CEU][hapmap]
rs1332662	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1332663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1332669	0.86[EUR][1000 genomes]
rs1412631	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs1412632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1412633	0.90[EUR][1000 genomes]
rs1412634	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1412639	0.86[EUR][1000 genomes]
rs1415217	0.87[CEU][hapmap]
rs1537319	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1556763	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap]
rs1571964	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1576878	0.86[EUR][1000 genomes]
rs1627765	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1759006	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1759007	0.90[EUR][1000 genomes]
rs1759008	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1759009	0.90[EUR][1000 genomes]
rs1759013	0.90[EUR][1000 genomes]
rs1764800	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs1794003	0.90[EUR][1000 genomes]
rs1794010	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1888991	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1953064	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2026429	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2151133	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2151134	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2151135	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2336595	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2336597	0.86[EUR][1000 genomes]
rs3891964	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4342879	0.87[CEU][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4350226	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs4556392	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs476390	0.87[CEU][hapmap]
rs4915148	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4915156	0.90[EUR][1000 genomes]
rs4915313	0.90[EUR][1000 genomes]
rs4915315	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4915316	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4915327	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4915337	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4915345	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4915378	0.83[ASW][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.83[YRI][hapmap]
rs4915379	0.89[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap]
rs5029273	0.84[YRI][hapmap]
rs510135	0.87[CEU][hapmap]
rs518149	0.87[CEU][hapmap]
rs5997	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6003	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs615647	0.87[CEU][hapmap]
rs616675	0.86[CEU][hapmap]
rs6428387	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6656448	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs6671696	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6677082	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6679189	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6680497	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6685259	0.90[EUR][1000 genomes]
rs6695300	0.96[EUR][1000 genomes]
rs6703400	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7411719	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7513826	0.87[CEU][hapmap]
rs7516700	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7520503	0.87[CEU][hapmap];1.00[GIH][hapmap]
rs7523013	0.87[CEU][hapmap]
rs7534353	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7539642	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7541429	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7542397	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7554757	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs857017	0.86[EUR][1000 genomes]
rs857020	0.83[EUR][1000 genomes]
rs857021	0.86[EUR][1000 genomes]
rs857022	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs857023	0.86[EUR][1000 genomes]
rs857026	0.86[EUR][1000 genomes]
rs857027	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs865071	0.85[EUR][1000 genomes]
rs877897	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs928439	1.00[CEU][hapmap]
rs928440	1.00[CEU][hapmap]
rs9427660	1.00[CEU][hapmap]
rs9427661	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs9427662	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs9427942	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs9726778	0.81[AMR][1000 genomes];0.93[EUR][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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873070	chr1:197079671-197165014	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv548871	chr1:197106604-197168233	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197052200-197114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:197054200-197113600	Weak transcription	Fetal Kidney	kidney
3	chr1:197055000-197114200	Weak transcription	Primary B cells from cord blood	blood
4	chr1:197073000-197115000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:197074000-197115000	Weak transcription	Fetal Brain Male	brain
6	chr1:197077000-197114200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:197095800-197114400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:197100400-197113600	Weak transcription	HSMM	muscle
9	chr1:197100800-197114200	Weak transcription	Fetal Intestine Large	intestine
10	chr1:197102600-197113800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:197104600-197113600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:197105400-197113600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:197107800-197113600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:197107800-197113800	Weak transcription	Fetal Intestine Small	intestine
15	chr1:197108000-197113800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr1:197108000-197115000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:197108400-197113600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:197108600-197113600	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:197108600-197113800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:197108600-197114000	Weak transcription	Fetal Stomach	stomach
21	chr1:197108600-197115000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:197108600-197115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:197109400-197115000	Weak transcription	HSMMtube	muscle
24	chr1:197109600-197113600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:197109600-197113600	Active TSS	GM12878-XiMat	blood
26	chr1:197109600-197113800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:197109600-197114200	Transcr. at gene 5' and 3'	Dnd41	blood
28	chr1:197109800-197113600	Weak transcription	Fetal Brain Female	brain
29	chr1:197110200-197113600	Weak transcription	Primary T cells from cord blood	blood
30	chr1:197111000-197113600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:197111200-197113600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:197111200-197113600	Weak transcription	Thymus	Thymus
33	chr1:197111400-197113800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:197111400-197115000	Weak transcription	Small Intestine	intestine
35	chr1:197111800-197113600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:197112200-197113600	Enhancers	Liver	Liver
37	chr1:197112200-197113600	Enhancers	HepG2	liver
38	chr1:197112400-197113600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:197112600-197113600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:197112600-197113600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:197112800-197113600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:197112800-197113600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:197112800-197113600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:197112800-197113600	Weak transcription	Fetal Lung	lung
45	chr1:197112800-197113600	Weak transcription	Fetal Thymus	thymus
46	chr1:197112800-197113600	Enhancers	Hela-S3	cervix
47	chr1:197112800-197113600	Weak transcription	Osteobl	bone
48	chr1:197112800-197113800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:197112800-197114200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
50	chr1:197113000-197113600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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