Variant report

Variant	rs12677
Chromosome Location	chr1:197053373-197053374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1034162	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10429911	0.87[CEU][hapmap]
rs10732295	0.87[CEU][hapmap];1.00[GIH][hapmap]
rs10732296	0.87[CEU][hapmap]
rs10733087	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10737687	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10754213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10754214	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10754215	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10754219	0.87[CEU][hapmap]
rs10801587	1.00[EUR][1000 genomes]
rs10801588	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10801590	1.00[EUR][1000 genomes]
rs10801591	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10922165	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10922166	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10922169	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1102176	0.82[AMR][1000 genomes]
rs1115246	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1115247	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1170878	0.86[EUR][1000 genomes]
rs1170880	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1170881	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1170882	0.86[EUR][1000 genomes]
rs1170883	0.86[EUR][1000 genomes]
rs12039586	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12092294	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs12731209	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1332662	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1332663	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1332669	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1412631	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1412632	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1412633	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1412634	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1412638	0.82[AMR][1000 genomes]
rs1412639	0.96[EUR][1000 genomes]
rs1415217	0.87[CEU][hapmap]
rs1537319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1556763	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap]
rs1571964	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1576878	0.96[EUR][1000 genomes]
rs1627765	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1759006	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1759007	1.00[EUR][1000 genomes]
rs1759008	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1759009	1.00[EUR][1000 genomes]
rs1759013	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1764800	0.87[CEU][hapmap]
rs1794003	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1794010	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1855116	0.86[EUR][1000 genomes]
rs1888991	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1953064	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2026429	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2151133	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2151134	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2151135	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2336595	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2336597	0.96[EUR][1000 genomes]
rs3891964	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4342879	0.87[CEU][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs4350226	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs4556392	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs476390	0.87[CEU][hapmap]
rs4915148	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915156	1.00[EUR][1000 genomes]
rs4915313	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915315	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915316	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915327	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915337	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915345	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4915378	1.00[GIH][hapmap];0.83[YRI][hapmap]
rs4915379	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs5029273	0.85[YRI][hapmap]
rs510135	0.87[CEU][hapmap]
rs518149	0.87[CEU][hapmap]
rs5997	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6003	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs615647	0.87[CEU][hapmap]
rs6428387	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6656448	0.85[CEU][hapmap];0.85[YRI][hapmap]
rs6656858	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]
rs6657171	0.86[EUR][1000 genomes]
rs6657246	0.86[EUR][1000 genomes]
rs6671696	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6677082	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6679189	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6680497	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6685259	1.00[EUR][1000 genomes]
rs6694672	0.86[EUR][1000 genomes]
rs6694853	0.86[EUR][1000 genomes]
rs6695300	0.93[EUR][1000 genomes]
rs6702340	0.86[EUR][1000 genomes]
rs6703400	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7411719	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7513826	0.87[CEU][hapmap]
rs7516700	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7520503	0.87[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs7523013	0.87[CEU][hapmap]
rs7534353	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7539642	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7541429	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7542397	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7554757	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs857017	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs857020	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs857021	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs857022	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs857023	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs857026	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs857027	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs865071	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs877897	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs928439	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs928440	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9427660	1.00[CEU][hapmap]
rs9427661	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs9427662	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs9427942	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs9726778	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv2756880	chr1:196709223-197066074	ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	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
6	nsv873065	chr1:197027749-197076194	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873067	chr1:197028634-197064496	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873068	chr1:197046782-197076194	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197050400-197055200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
2	chr1:197050400-197065600	Weak transcription	Stomach Mucosa	stomach
3	chr1:197050600-197055200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr1:197050600-197055400	ZNF genes & repeats	Dnd41	blood
5	chr1:197050600-197059600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:197050600-197064400	Weak transcription	Fetal Heart	heart
7	chr1:197050800-197053600	Weak transcription	Gastric	stomach
8	chr1:197050800-197055600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:197050800-197057200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:197051000-197054800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
11	chr1:197051000-197054800	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr1:197051000-197055600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:197051200-197054000	Weak transcription	NH-A	brain
14	chr1:197051400-197054200	Strong transcription	Fetal Kidney	kidney
15	chr1:197051400-197055200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:197051400-197063000	Strong transcription	HUVEC	blood vessel
17	chr1:197051400-197069600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:197051600-197053600	Weak transcription	NHEK	skin
19	chr1:197051600-197054600	Strong transcription	Fetal Intestine Large	intestine
20	chr1:197051600-197055000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:197051600-197057000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr1:197051600-197057200	Strong transcription	NHDF-Ad	bronchial
23	chr1:197051600-197065600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:197051600-197066200	Strong transcription	Hela-S3	cervix
25	chr1:197051800-197055000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:197051800-197055600	Strong transcription	HMEC	breast
27	chr1:197051800-197057000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:197051800-197061000	Strong transcription	Osteobl	bone
29	chr1:197051800-197069800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:197052000-197054800	Weak transcription	Fetal Brain Male	brain
31	chr1:197052000-197055000	Strong transcription	Primary B cells from cord blood	blood
32	chr1:197052000-197062000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:197052000-197064200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:197052200-197053600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:197052200-197053800	Weak transcription	HepG2	liver
36	chr1:197052200-197054000	Strong transcription	Brain Germinal Matrix	brain
37	chr1:197052200-197054000	Weak transcription	Placenta	Placenta
38	chr1:197052200-197054200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:197052200-197054600	Strong transcription	Fetal Muscle Leg	muscle
40	chr1:197052200-197054600	Strong transcription	Thymus	Thymus
41	chr1:197052200-197054800	Strong transcription	GM12878-XiMat	blood
42	chr1:197052200-197055600	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr1:197052200-197055600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:197052200-197055600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:197052200-197057000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:197052200-197057000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:197052200-197058000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr1:197052200-197061400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:197052200-197062200	Weak transcription	Fetal Intestine Small	intestine
50	chr1:197052200-197063200	Strong transcription	Primary hematopoietic stem cells	blood

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