Variant report

Variant	rs236993
Chromosome Location	chr4:88016874-88016875
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88016859..88019570-chr4:88023284..88025236,3	MCF-7	breast:
2	chr4:87926587..87929393-chr4:88014126..88017404,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10023050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1037814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097127	0.84[CEU][hapmap];0.86[CHB][hapmap];0.96[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11946481	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1408	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1674999	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16930	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs17012368	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2045592	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2125787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236987	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28432336	0.83[ASN][1000 genomes]
rs28677145	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2926511	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs342435	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs342437	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342454	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736669	0.84[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3775214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775217	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775220	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775221	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775223	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs442177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4693156	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72877984	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7660883	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9998251	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:87995800-88023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:87996800-88023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:88000400-88020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:88001400-88025200	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:88001800-88025200	Weak transcription	Gastric	stomach
8	chr4:88003400-88028600	Weak transcription	HSMMtube	muscle
9	chr4:88004200-88019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:88004400-88025200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:88005000-88017400	Strong transcription	Dnd41	blood
12	chr4:88007600-88018200	Weak transcription	Thymus	Thymus
13	chr4:88009000-88017800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:88009400-88017600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:88010200-88018200	Weak transcription	Lung	lung
16	chr4:88010600-88018400	Strong transcription	Fetal Thymus	thymus
17	chr4:88011600-88019000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:88011800-88022400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:88011800-88032800	Weak transcription	Colonic Mucosa	Colon
20	chr4:88012000-88018000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:88012000-88021400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:88013600-88018000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:88014000-88021400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:88014200-88017400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr4:88014200-88018000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:88014200-88018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:88014400-88019000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:88014400-88019000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr4:88014400-88020600	Weak transcription	Pancreas	Pancrea
30	chr4:88014400-88020600	Weak transcription	Spleen	Spleen
31	chr4:88014400-88024600	Weak transcription	HSMM	muscle
32	chr4:88014600-88017800	Weak transcription	Ovary	ovary
33	chr4:88014600-88018600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr4:88014600-88020200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr4:88014800-88017000	Strong transcription	K562	blood
36	chr4:88014800-88017400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:88014800-88018200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:88014800-88018200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:88014800-88019200	Weak transcription	Fetal Kidney	kidney
40	chr4:88014800-88020600	Weak transcription	Right Atrium	heart
41	chr4:88014800-88024400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:88014800-88024600	Weak transcription	Stomach Mucosa	stomach
43	chr4:88014800-88024800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr4:88015000-88017200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr4:88015000-88017200	Strong transcription	Adipose Nuclei	Adipose
46	chr4:88015000-88017200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:88015000-88018000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr4:88015000-88018200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:88015000-88021000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:88015000-88024000	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links