Variant report

Variant	rs12572387
Chromosome Location	chr10:52347599-52347600
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52345136..52347979-chr10:52349121..52350897,2	MCF-7	breast:
2	chr10:52287492..52289090-chr10:52346967..52349226,2	K562	blood:
3	chr10:52343887..52348125-chr10:52383719..52386062,5	K562	blood:
4	chr10:52346092..52348176-chr10:52375554..52378162,2	K562	blood:
5	chr10:52346537..52348332-chr10:52378536..52380819,2	K562	blood:
6	chr10:52342227..52348125-chr10:52381237..52386507,8	K562	blood:
7	chr10:52346124..52348507-chr10:52350618..52352666,3	K562	blood:
8	chr10:52346285..52348246-chr10:52382049..52384248,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000238523	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1010930	0.90[ASN][1000 genomes]
rs10763535	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs10763550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10763560	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10763566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826149	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs10826155	0.88[ASN][1000 genomes]
rs10826159	0.89[ASN][1000 genomes]
rs10826160	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10826161	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10826163	0.90[ASN][1000 genomes]
rs10826164	0.90[ASN][1000 genomes]
rs10826165	0.90[ASN][1000 genomes]
rs10826166	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10826167	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10826170	0.84[ASN][1000 genomes]
rs10826228	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006084	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11006114	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11006118	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11006141	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11006160	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006201	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11006217	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12219692	0.83[CEU][hapmap]
rs12415817	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12415836	0.90[ASN][1000 genomes]
rs12570382	0.87[YRI][hapmap]
rs1884570	0.90[ASN][1000 genomes]
rs2144861	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2224249	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3011777	0.86[CHB][hapmap]
rs34659292	0.90[ASN][1000 genomes]
rs36122110	0.90[ASN][1000 genomes]
rs4519042	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4519043	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4935173	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs4935174	0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4935733	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs7074764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078284	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7088141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094143	0.90[ASN][1000 genomes]
rs7893884	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs7900424	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7907260	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7915606	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7916397	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs9299582	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs9919413	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][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	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
8	nsv971909	chr10:52344351-52348873	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52322000-52348600	Weak transcription	Fetal Stomach	stomach
2	chr10:52336200-52349000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr10:52336400-52348600	Weak transcription	Lung	lung
4	chr10:52336800-52363000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:52337000-52348000	Weak transcription	Thymus	Thymus
6	chr10:52337800-52347800	Weak transcription	Fetal Thymus	thymus
7	chr10:52337800-52352800	Weak transcription	Fetal Brain Male	brain
8	chr10:52338000-52356400	Weak transcription	Fetal Brain Female	brain
9	chr10:52338000-52363800	Weak transcription	Fetal Kidney	kidney
10	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
11	chr10:52338200-52347600	Weak transcription	Fetal Muscle Leg	muscle
12	chr10:52338200-52347800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:52338200-52348800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr10:52338200-52353600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:52338200-52353800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr10:52338400-52348000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr10:52338600-52347600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr10:52338600-52353400	Weak transcription	Brain Germinal Matrix	brain
19	chr10:52338600-52353600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr10:52338800-52347800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr10:52338800-52348000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr10:52340400-52360200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr10:52341000-52347600	Weak transcription	Fetal Lung	lung
24	chr10:52341000-52348000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr10:52341200-52347800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr10:52341200-52348800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr10:52341400-52347800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr10:52341400-52355400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:52341400-52360200	Weak transcription	GM12878-XiMat	blood
31	chr10:52341600-52347800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr10:52341600-52348600	Weak transcription	Fetal Intestine Small	intestine
33	chr10:52341800-52350600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr10:52341800-52351800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:52341800-52352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr10:52341800-52355000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr10:52341800-52362000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr10:52342000-52347600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr10:52342000-52352000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr10:52342200-52347600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr10:52342200-52351800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:52342400-52347800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr10:52342400-52348000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr10:52342400-52351600	Weak transcription	Brain Angular Gyrus	brain
45	chr10:52342400-52353000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr10:52342600-52356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr10:52342800-52348400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr10:52342800-52360200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr10:52343000-52349000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr10:52343000-52353000	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links