Variant report

Variant	rs1660742
Chromosome Location	chr1:9881965-9881966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9881352..9884024-chr1:9922177..9924275,2	K562	blood:
2	chr1:9875644..9877842-chr1:9881714..9883858,3	MCF-7	breast:
3	chr1:9881290..9883388-chr1:9900739..9903390,2	MCF-7	breast:
4	chr1:9881807..9884566-chr1:10002965..10004897,2	K562	blood:
5	chr1:9881807..9884566-chr1:10002290..10004897,3	K562	blood:
6	chr1:9879335..9882157-chr1:9882650..9885609,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173614	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10779730	0.88[ASN][1000 genomes]
rs10779731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10864435	0.83[CHD][hapmap];0.83[MEX][hapmap]
rs10864436	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs10864437	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10864438	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121484	0.83[CHD][hapmap]
rs11121486	0.88[ASW][hapmap];0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs11121489	0.90[ASN][1000 genomes]
rs11121490	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11121492	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11121493	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11674	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11804356	0.90[ASN][1000 genomes]
rs11806520	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12021914	0.90[ASN][1000 genomes]
rs12034239	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12037599	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs12042293	0.88[ASW][hapmap];0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs12047054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12064975	0.90[ASN][1000 genomes]
rs12078414	1.00[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs12087051	0.91[EUR][1000 genomes]
rs12088273	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1220419	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1228434	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12568720	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12569008	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1615629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1631962	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1660741	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];1.00[ASN][1000 genomes]
rs17034335	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17034340	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1767277	1.00[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs2788605	0.86[EUR][1000 genomes]
rs4512653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4585981	0.86[EUR][1000 genomes]
rs56109009	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57560942	0.95[EUR][1000 genomes]
rs59729812	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6666296	0.88[CHB][hapmap]
rs6677664	0.88[CHB][hapmap]
rs6699320	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72855716	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72855733	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs72855735	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72855745	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs72855747	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7526958	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7550246	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7550295	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs767762	1.00[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs935071	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9859000-9882400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:9865000-9882200	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:9865600-9882200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:9868200-9882600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:9868400-9882600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:9869200-9882600	Weak transcription	Esophagus	oesophagus
7	chr1:9869400-9882600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:9869600-9882000	Weak transcription	NHLF	lung
9	chr1:9869600-9882400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:9869800-9882200	Weak transcription	Fetal Thymus	thymus
11	chr1:9869800-9882400	Weak transcription	Thymus	Thymus
12	chr1:9869800-9882600	Weak transcription	Right Atrium	heart
13	chr1:9869800-9882800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:9870000-9882400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:9872400-9882600	Weak transcription	Right Ventricle	heart
16	chr1:9872600-9882400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:9873600-9883000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:9874400-9882000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:9875200-9882600	Weak transcription	Placenta	Placenta
20	chr1:9876600-9882000	Weak transcription	Osteobl	bone
21	chr1:9876600-9882200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:9877200-9882200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:9877200-9882200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:9877200-9882600	Weak transcription	Ovary	ovary
25	chr1:9877800-9882000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:9878000-9882000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:9878000-9882200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:9879000-9882600	Enhancers	Primary B cells from peripheral blood	blood
29	chr1:9879000-9882600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr1:9879200-9882400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:9879400-9882400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:9880200-9884400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:9880400-9882400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr1:9880600-9882000	Enhancers	Fetal Brain Male	brain
35	chr1:9880600-9882200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:9880600-9882200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:9880800-9882000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:9880800-9882000	Enhancers	Fetal Brain Female	brain
39	chr1:9880800-9882200	Enhancers	Hela-S3	cervix
40	chr1:9880800-9882400	Active TSS	Brain Angular Gyrus	brain
41	chr1:9880800-9882400	Enhancers	Fetal Intestine Small	intestine
42	chr1:9880800-9882800	Weak transcription	Pancreas	Pancrea
43	chr1:9880800-9883000	Flanking Active TSS	Dnd41	blood
44	chr1:9881000-9882000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:9881000-9882400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:9881000-9882800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:9881200-9882000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr1:9881200-9882000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:9881200-9882200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:9881200-9884400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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