Variant report

Variant	rs6685259
Chromosome Location	chr1:197093098-197093099
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197090506..197092545-chr1:197093003..197095180,2	MCF-7	breast:
2	chr1:197093048..197099045-chr1:197107378..197117076,12	K562	blood:
3	chr1:197092500..197094237-chr1:197110834..197113696,2	K562	blood:

Variant related genes	Relation type
ENSG00000066279	Chromatin interaction
ENSG00000235748	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1034162	1.00[EUR][1000 genomes]
rs10733087	1.00[EUR][1000 genomes]
rs10737687	0.91[EUR][1000 genomes]
rs10754213	1.00[EUR][1000 genomes]
rs10754214	1.00[EUR][1000 genomes]
rs10754215	1.00[EUR][1000 genomes]
rs10801587	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10801588	1.00[EUR][1000 genomes]
rs10801590	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10801591	1.00[EUR][1000 genomes]
rs10922165	0.98[EUR][1000 genomes]
rs10922166	1.00[EUR][1000 genomes]
rs10922169	0.93[EUR][1000 genomes]
rs1115246	0.95[EUR][1000 genomes]
rs1115247	1.00[EUR][1000 genomes]
rs1170878	0.86[EUR][1000 genomes]
rs1170880	0.86[EUR][1000 genomes]
rs1170881	0.86[EUR][1000 genomes]
rs1170882	0.86[EUR][1000 genomes]
rs1170883	0.86[EUR][1000 genomes]
rs12039586	0.93[EUR][1000 genomes]
rs12092294	0.86[EUR][1000 genomes]
rs12677	1.00[EUR][1000 genomes]
rs12731209	0.86[EUR][1000 genomes]
rs1332662	0.93[EUR][1000 genomes]
rs1332663	0.93[EUR][1000 genomes]
rs1332669	0.96[EUR][1000 genomes]
rs1412631	1.00[EUR][1000 genomes]
rs1412632	1.00[EUR][1000 genomes]
rs1412633	1.00[EUR][1000 genomes]
rs1412634	1.00[EUR][1000 genomes]
rs1412639	0.96[EUR][1000 genomes]
rs1537319	1.00[EUR][1000 genomes]
rs1571964	0.90[EUR][1000 genomes]
rs1576878	0.96[EUR][1000 genomes]
rs1627765	1.00[EUR][1000 genomes]
rs1759006	1.00[EUR][1000 genomes]
rs1759007	1.00[EUR][1000 genomes]
rs1759008	1.00[EUR][1000 genomes]
rs1759009	1.00[EUR][1000 genomes]
rs1759013	1.00[EUR][1000 genomes]
rs1794003	1.00[EUR][1000 genomes]
rs1794010	1.00[EUR][1000 genomes]
rs1855116	0.86[EUR][1000 genomes]
rs1888991	0.93[EUR][1000 genomes]
rs1953064	1.00[EUR][1000 genomes]
rs2026429	1.00[EUR][1000 genomes]
rs2151133	1.00[EUR][1000 genomes]
rs2151134	0.91[EUR][1000 genomes]
rs2151135	0.93[EUR][1000 genomes]
rs2336595	0.96[EUR][1000 genomes]
rs2336597	0.96[EUR][1000 genomes]
rs3891964	1.00[EUR][1000 genomes]
rs4342879	0.81[EUR][1000 genomes]
rs4350226	0.81[EUR][1000 genomes]
rs4556392	0.93[EUR][1000 genomes]
rs4915148	1.00[EUR][1000 genomes]
rs4915156	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4915313	1.00[EUR][1000 genomes]
rs4915315	1.00[EUR][1000 genomes]
rs4915316	1.00[EUR][1000 genomes]
rs4915327	1.00[EUR][1000 genomes]
rs4915337	1.00[EUR][1000 genomes]
rs4915345	0.93[EUR][1000 genomes]
rs5997	1.00[EUR][1000 genomes]
rs6003	1.00[EUR][1000 genomes]
rs6428387	1.00[EUR][1000 genomes]
rs6656858	0.90[EUR][1000 genomes]
rs6657171	0.86[EUR][1000 genomes]
rs6657246	0.86[EUR][1000 genomes]
rs6671696	1.00[EUR][1000 genomes]
rs6677082	0.90[EUR][1000 genomes]
rs6679189	0.93[EUR][1000 genomes]
rs6680497	1.00[EUR][1000 genomes]
rs6694672	0.86[EUR][1000 genomes]
rs6694853	0.86[EUR][1000 genomes]
rs6695300	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6702340	0.86[EUR][1000 genomes]
rs6703400	1.00[EUR][1000 genomes]
rs7411719	1.00[EUR][1000 genomes]
rs7516700	0.93[EUR][1000 genomes]
rs7534353	0.90[EUR][1000 genomes]
rs7539642	1.00[EUR][1000 genomes]
rs7541429	0.91[EUR][1000 genomes]
rs7542397	0.90[EUR][1000 genomes]
rs7554757	0.91[EUR][1000 genomes]
rs857017	0.96[EUR][1000 genomes]
rs857020	0.93[EUR][1000 genomes]
rs857021	0.96[EUR][1000 genomes]
rs857022	0.96[EUR][1000 genomes]
rs857023	0.96[EUR][1000 genomes]
rs857026	0.96[EUR][1000 genomes]
rs857027	0.96[EUR][1000 genomes]
rs865071	0.95[EUR][1000 genomes]
rs877897	0.90[EUR][1000 genomes]
rs928439	0.86[EUR][1000 genomes]
rs928440	0.86[EUR][1000 genomes]
rs9427661	0.86[EUR][1000 genomes]
rs9427662	0.86[EUR][1000 genomes]
rs9427942	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	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	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
6	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
7	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
8	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

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197052200-197106600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:197052200-197114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:197054200-197113600	Weak transcription	Fetal Kidney	kidney
4	chr1:197055000-197114200	Weak transcription	Primary B cells from cord blood	blood
5	chr1:197070600-197100000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:197071000-197105400	Strong transcription	Dnd41	blood
7	chr1:197071400-197095800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:197071800-197104600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:197072600-197104600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:197072600-197107400	Weak transcription	Fetal Intestine Small	intestine
11	chr1:197073000-197104000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:197073000-197115000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:197073600-197098400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:197074000-197115000	Weak transcription	Fetal Brain Male	brain
15	chr1:197074200-197102000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:197076200-197094000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:197076400-197096400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:197077000-197114200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:197078200-197100400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:197080600-197105400	Strong transcription	Fetal Thymus	thymus
21	chr1:197081200-197103000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:197082000-197094600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:197083600-197098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:197083600-197108000	Strong transcription	HUVEC	blood vessel
25	chr1:197083800-197095200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:197084000-197099000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:197084200-197094200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr1:197084200-197098400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:197084200-197098600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:197084400-197102000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:197084400-197106600	Weak transcription	Fetal Stomach	stomach
32	chr1:197084600-197100000	Strong transcription	Hela-S3	cervix
33	chr1:197085000-197095800	Strong transcription	A549	lung
34	chr1:197085800-197099800	Weak transcription	Fetal Heart	heart
35	chr1:197085800-197099800	Weak transcription	Thymus	Thymus
36	chr1:197085800-197109600	Weak transcription	Brain Germinal Matrix	brain
37	chr1:197085800-197111000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:197087600-197098600	Weak transcription	Fetal Lung	lung
39	chr1:197087800-197098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:197089200-197098600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:197089200-197105200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:197089800-197101000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:197089800-197105200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:197089800-197108400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:197090000-197110800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:197090200-197098600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:197090400-197101000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:197090600-197094400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:197090600-197094400	Strong transcription	NHDF-Ad	bronchial
50	chr1:197090600-197098600	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links