Variant report

Variant	rs1332660
Chromosome Location	chr1:197053141-197053142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10737686	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10801582	0.86[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs10801583	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10801584	0.82[AMR][1000 genomes]
rs10801586	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10922151	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10922162	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10922167	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10922168	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10922177	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs10922179	0.87[EUR][1000 genomes]
rs12028827	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12034362	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12042442	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12075161	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12085377	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12116643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12128631	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12134960	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12137359	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1332664	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1412636	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2298883	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4639796	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4915344	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5993	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61819092	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72738632	0.93[EUR][1000 genomes];0.85[ASN][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	chr1:197051400-197053200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
15	chr1:197051400-197054200	Strong transcription	Fetal Kidney	kidney
16	chr1:197051400-197055200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:197051400-197063000	Strong transcription	HUVEC	blood vessel
18	chr1:197051400-197069600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:197051600-197053600	Weak transcription	NHEK	skin
20	chr1:197051600-197054600	Strong transcription	Fetal Intestine Large	intestine
21	chr1:197051600-197055000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:197051600-197057000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:197051600-197057200	Strong transcription	NHDF-Ad	bronchial
24	chr1:197051600-197065600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:197051600-197066200	Strong transcription	Hela-S3	cervix
26	chr1:197051800-197055000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:197051800-197055600	Strong transcription	HMEC	breast
28	chr1:197051800-197057000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:197051800-197061000	Strong transcription	Osteobl	bone
30	chr1:197051800-197069800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:197052000-197054800	Weak transcription	Fetal Brain Male	brain
32	chr1:197052000-197055000	Strong transcription	Primary B cells from cord blood	blood
33	chr1:197052000-197062000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:197052000-197064200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:197052200-197053600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:197052200-197053800	Weak transcription	HepG2	liver
37	chr1:197052200-197054000	Strong transcription	Brain Germinal Matrix	brain
38	chr1:197052200-197054000	Weak transcription	Placenta	Placenta
39	chr1:197052200-197054200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:197052200-197054600	Strong transcription	Fetal Muscle Leg	muscle
41	chr1:197052200-197054600	Strong transcription	Thymus	Thymus
42	chr1:197052200-197054800	Strong transcription	GM12878-XiMat	blood
43	chr1:197052200-197055600	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr1:197052200-197055600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:197052200-197055600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:197052200-197057000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:197052200-197057000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:197052200-197058000	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr1:197052200-197061400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:197052200-197062200	Weak transcription	Fetal Intestine Small	intestine

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