Variant report

Variant	rs1257008
Chromosome Location	chr2:97634672-97634673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97631877..97635109-chr2:97650329..97653813,3	MCF-7	breast:
2	chr2:97497462..97499468-chr2:97634346..97637151,2	MCF-7	breast:
3	chr2:97623724..97626251-chr2:97633605..97636499,4	K562	blood:

Variant related genes	Relation type
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10202644	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1257000	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1257009	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1257011	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1257012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1257015	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1257016	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1257017	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1257018	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1257019	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1257020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1257027	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1257028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1257029	0.91[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1257114	0.87[ASN][1000 genomes]
rs1268682	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12717787	0.92[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13016654	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13021723	0.96[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1623881	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1624844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1730106	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1730111	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1730119	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1730120	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1730122	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1730123	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1730124	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1730126	0.96[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1730128	0.96[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1730129	0.95[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1730130	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1730131	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1796027	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1796028	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1796029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1796032	0.91[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1796038	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1796041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1796044	0.96[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1796045	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1796046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1796047	0.96[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1796049	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2707304	0.92[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]
rs34434950	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4263148	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4366944	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4586672	0.91[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6576992	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6576993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6576994	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6576995	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6576997	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6576999	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6707255	0.85[AMR][1000 genomes]
rs6714860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6715329	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6725927	0.83[CHB][hapmap]
rs6757916	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7569434	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7584318	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7584335	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7593493	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7597743	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv1001432	chr2:97591069-97671395	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	esv32727	chr2:97616488-97643975	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1257008		cis	Lymphoblastoid	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97620800-97643600	Weak transcription	Right Atrium	heart
2	chr2:97626200-97635800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:97630600-97635600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:97630600-97635600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:97630600-97635600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr2:97630600-97635800	Weak transcription	Colonic Mucosa	Colon
7	chr2:97630600-97635800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:97630600-97636000	Weak transcription	Fetal Intestine Small	intestine
9	chr2:97630800-97635600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:97630800-97636200	Weak transcription	Fetal Intestine Large	intestine
11	chr2:97631200-97635400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:97631600-97635800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:97631800-97637000	Enhancers	Brain Substantia Nigra	brain
14	chr2:97631800-97637400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr2:97632000-97636600	Enhancers	Brain Anterior Caudate	brain
16	chr2:97632200-97635200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:97632200-97636400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:97632200-97636800	Enhancers	Brain Cingulate Gyrus	brain
19	chr2:97632400-97636400	Enhancers	Brain Angular Gyrus	brain
20	chr2:97633000-97635400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:97633200-97635600	Weak transcription	Primary T cells from cord blood	blood
22	chr2:97633200-97635800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:97633200-97643200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:97633400-97635800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:97633400-97635800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:97633400-97635800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:97633600-97635400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr2:97634000-97637200	Enhancers	Brain Hippocampus Middle	brain
29	chr2:97634600-97642200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links