Variant report

Variant	rs12358866
Chromosome Location	chr10:52373976-52373977
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52373141..52377774-chr10:52378271..52384648,13	K562	blood:
2	chr10:52369031..52370676-chr10:52373294..52376073,2	MCF-7	breast:
3	chr10:52340715..52342372-chr10:52372792..52375032,2	MCF-7	breast:
4	chr10:52361957..52364109-chr10:52372914..52375707,2	K562	blood:
5	chr10:52321910..52324715-chr10:52371827..52374232,3	K562	blood:
6	chr10:52371729..52375098-chr10:52383274..52385073,4	MCF-7	breast:
7	chr10:52371171..52374113-chr10:52380759..52382982,2	MCF-7	breast:
8	chr10:52372893..52376676-chr10:52385065..52387133,3	K562	blood:
9	chr10:52366580..52370875-chr10:52371309..52374318,4	K562	blood:
10	chr10:52371856..52377048-chr10:52377440..52385994,18	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10826243	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826273	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11006328	0.92[ASN][1000 genomes]
rs11006358	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11006369	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11006427	0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs11006433	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11006434	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11006437	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11006441	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11006452	0.92[ASN][1000 genomes]
rs11006469	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11006470	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs11006473	0.83[ASN][1000 genomes]
rs11006474	0.85[ASN][1000 genomes]
rs11006476	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11006477	0.85[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs11006479	0.92[ASN][1000 genomes]
rs11006493	0.87[ASN][1000 genomes]
rs12358192	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358348	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12360512	0.85[ASN][1000 genomes]
rs13376734	0.83[YRI][hapmap]
rs17581567	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17582633	0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs3001853	0.83[YRI][hapmap]
rs3001854	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3001865	0.89[YRI][hapmap]
rs3011728	0.81[AFR][1000 genomes]
rs55763387	0.92[ASN][1000 genomes]
rs55953936	0.92[ASN][1000 genomes]
rs55969688	0.92[ASN][1000 genomes]
rs56029434	0.92[ASN][1000 genomes]
rs56044934	0.88[ASN][1000 genomes]
rs56138205	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56306926	0.88[ASN][1000 genomes]
rs60177889	0.92[ASN][1000 genomes]
rs7093195	1.00[CEU][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7096920	0.83[YRI][hapmap]
rs7097359	0.82[YRI][hapmap]
rs7897345	0.83[YRI][hapmap]
rs7904306	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52360200-52375600	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr10:52364400-52374400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr10:52365200-52374000	Weak transcription	Placenta	Placenta
4	chr10:52365400-52375000	Weak transcription	Fetal Brain Female	brain
5	chr10:52365400-52379400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr10:52365600-52377200	Weak transcription	Primary T cells from cord blood	blood
7	chr10:52365800-52378200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:52366000-52381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr10:52366600-52377800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:52367200-52377800	Weak transcription	Primary B cells from cord blood	blood
11	chr10:52367200-52379400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr10:52367400-52381400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:52367600-52378400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr10:52367600-52381400	Weak transcription	NHLF	lung
15	chr10:52367600-52381400	Weak transcription	Osteobl	bone
16	chr10:52368000-52374200	Weak transcription	Stomach Mucosa	stomach
17	chr10:52368200-52375400	Enhancers	Pancreas	Pancrea
18	chr10:52369000-52378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr10:52369200-52375800	Enhancers	Fetal Heart	heart
20	chr10:52369400-52375400	Enhancers	Brain Anterior Caudate	brain
21	chr10:52369600-52374200	Enhancers	Fetal Lung	lung
22	chr10:52369600-52374800	Enhancers	Brain Cingulate Gyrus	brain
23	chr10:52369600-52375400	Enhancers	Psoas Muscle	Psoas
24	chr10:52369600-52375400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr10:52369600-52375800	Enhancers	Brain Angular Gyrus	brain
26	chr10:52369600-52375800	Enhancers	Brain Hippocampus Middle	brain
27	chr10:52369800-52374400	Enhancers	Brain Substantia Nigra	brain
28	chr10:52369800-52376200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr10:52370200-52378400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:52370600-52374400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:52370800-52378400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr10:52371000-52381200	Weak transcription	Fetal Stomach	stomach
33	chr10:52371200-52374000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr10:52371200-52374400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr10:52371200-52378200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr10:52371200-52381600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr10:52371400-52375400	Enhancers	Liver	Liver
38	chr10:52371600-52374800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr10:52371600-52374800	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr10:52371600-52375000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr10:52371800-52374000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr10:52371800-52374000	Weak transcription	Spleen	Spleen
43	chr10:52371800-52375600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr10:52371800-52378400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr10:52372000-52374000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr10:52372000-52374200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr10:52372000-52374400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr10:52372000-52374600	Enhancers	GM12878-XiMat	blood
49	chr10:52372000-52375200	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr10:52372200-52374200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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