Variant report

Variant	rs7539642
Chromosome Location	chr1:197063841-197063842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197055379..197060712-chr1:197061077..197065456,6	K562	blood:
2	chr1:197056210..197058041-chr1:197063459..197065342,2	K562	blood:

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1034162	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10733087	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10737687	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10754213	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10754214	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10754215	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10801587	1.00[EUR][1000 genomes]
rs10801588	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10801590	1.00[EUR][1000 genomes]
rs10801591	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10922165	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10922166	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10922169	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1115246	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1115247	0.85[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1170878	0.86[EUR][1000 genomes]
rs1170880	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1170881	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1170882	0.86[EUR][1000 genomes]
rs1170883	0.86[EUR][1000 genomes]
rs12039586	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12092294	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs12677	0.85[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12731209	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1332662	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1332663	0.85[CEU][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1332669	0.96[EUR][1000 genomes]
rs1412631	0.85[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1412632	0.85[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1412633	1.00[EUR][1000 genomes]
rs1412634	0.85[CEU][hapmap];1.00[EUR][1000 genomes]
rs1412639	0.96[EUR][1000 genomes]
rs1537319	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1571964	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1576878	0.96[EUR][1000 genomes]
rs1627765	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1759006	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1759007	1.00[EUR][1000 genomes]
rs1759008	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1759009	1.00[EUR][1000 genomes]
rs1759013	1.00[EUR][1000 genomes]
rs1794003	1.00[EUR][1000 genomes]
rs1794010	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1855116	0.86[EUR][1000 genomes]
rs1888991	0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1953064	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2026429	0.85[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2151133	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2151134	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2151135	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2336595	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2336597	0.96[EUR][1000 genomes]
rs3891964	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4342879	0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs4350226	0.81[EUR][1000 genomes]
rs4556392	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4915148	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915156	1.00[EUR][1000 genomes]
rs4915313	1.00[EUR][1000 genomes]
rs4915315	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915316	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915327	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915337	0.85[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915345	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5029273	0.81[YRI][hapmap]
rs5997	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6003	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6428387	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6656448	0.81[YRI][hapmap]
rs6656858	0.85[CEU][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6657171	0.86[EUR][1000 genomes]
rs6657246	0.86[EUR][1000 genomes]
rs6671696	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6677082	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6679189	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6680497	0.89[AFR][1000 genomes];1.00[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	0.85[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7411719	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7516700	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7534353	0.85[CEU][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7541429	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7542397	0.85[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7554757	0.91[EUR][1000 genomes]
rs857017	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs857020	0.93[EUR][1000 genomes]
rs857021	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs857022	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs857023	0.96[EUR][1000 genomes]
rs857026	0.96[EUR][1000 genomes]
rs857027	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs865071	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs877897	0.85[CEU][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs928439	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs928440	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs9427660	0.85[CEU][hapmap]
rs9427661	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs9427662	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs9427942	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs9726778	0.83[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	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
9	nsv873069	chr1:197055925-197109042	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197050400-197065600	Weak transcription	Stomach Mucosa	stomach
2	chr1:197050600-197064400	Weak transcription	Fetal Heart	heart
3	chr1:197051400-197069600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:197051600-197065600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:197051600-197066200	Strong transcription	Hela-S3	cervix
6	chr1:197051800-197069800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:197052000-197064200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:197052200-197064600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:197052200-197065400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:197052200-197065400	Weak transcription	Fetal Brain Female	brain
11	chr1:197052200-197074400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:197052200-197076200	Weak transcription	NHLF	lung
13	chr1:197052200-197083600	Weak transcription	Fetal Stomach	stomach
14	chr1:197052200-197106600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:197052200-197114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:197052400-197065400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:197052400-197068800	Weak transcription	Primary T cells from cord blood	blood
18	chr1:197052400-197069200	Strong transcription	Fetal Thymus	thymus
19	chr1:197052600-197068600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:197052800-197067000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:197053000-197064800	Strong transcription	K562	blood
22	chr1:197053000-197066800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:197053000-197067000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:197054000-197071200	Weak transcription	Brain Germinal Matrix	brain
25	chr1:197054200-197066600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:197054200-197071200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:197054200-197113600	Weak transcription	Fetal Kidney	kidney
28	chr1:197054600-197072400	Weak transcription	Thymus	Thymus
29	chr1:197054800-197065400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:197054800-197066200	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:197055000-197114200	Weak transcription	Primary B cells from cord blood	blood
32	chr1:197055200-197064600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:197055200-197068200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:197055400-197069400	Strong transcription	Dnd41	blood
35	chr1:197055600-197068600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:197055600-197074000	Weak transcription	Placenta	Placenta
37	chr1:197057000-197069200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:197057200-197071800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:197057200-197073200	Weak transcription	NHEK	skin
40	chr1:197057800-197069800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:197058400-197065600	Strong transcription	NHDF-Ad	bronchial
42	chr1:197058800-197070800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:197059600-197069200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:197060000-197073800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:197060400-197071200	Weak transcription	Fetal Lung	lung
46	chr1:197060400-197072400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:197060600-197064000	Strong transcription	HMEC	breast
48	chr1:197061000-197067400	Weak transcription	HSMM	muscle
49	chr1:197061000-197068800	Weak transcription	Osteobl	bone
50	chr1:197061200-197073200	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links