Variant report

Variant	rs1203415
Chromosome Location	chr10:52175784-52175785
allele	A/C
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52173595..52180106-chr10:52381535..52385847,7	MCF-7	breast:
2	chr10:52173619..52179913-chr10:52381938..52386991,6	K562	blood:
3	chr10:52152378..52155454-chr10:52174313..52178963,4	MCF-7	breast:
4	chr10:52164630..52167501-chr10:52173843..52176462,2	MCF-7	breast:
5	chr10:52173349..52175159-chr10:52175578..52178225,2	K562	blood:
6	chr10:52152624..52157680-chr10:52173844..52179255,6	K562	blood:
7	chr10:52175389..52176966-chr10:52179598..52182050,2	K562	blood:
8	chr10:52136978..52138506-chr10:52174976..52177884,2	K562	blood:
9	chr10:52084222..52086810-chr10:52173871..52176505,2	K562	blood:
10	chr10:52164112..52165618-chr10:52174506..52177347,2	K562	blood:
11	chr10:52174976..52177960-chr10:52379518..52382234,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000269700	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1011881	0.86[JPT][hapmap]
rs10740714	0.86[ASN][1000 genomes]
rs10763366	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs10763529	0.86[JPT][hapmap]
rs10826100	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10826118	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10826126	0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11005937	0.86[ASN][1000 genomes]
rs1203377	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203418	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs1203420	0.97[EUR][1000 genomes]
rs1203421	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs1436206	0.82[YRI][hapmap]
rs1548256	0.80[JPT][hapmap]
rs1569962	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1569963	0.86[ASN][1000 genomes]
rs1740761	0.82[CEU][hapmap]
rs1916566	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1916567	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2092996	0.86[JPT][hapmap]
rs2099527	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2117958	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2144862	0.86[JPT][hapmap]
rs2339402	0.96[EUR][1000 genomes]
rs2339505	0.82[JPT][hapmap]
rs2339506	0.80[JPT][hapmap]
rs2574959	0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2574985	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs2688878	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2842103	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2842108	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2842111	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2983350	0.80[CEU][hapmap]
rs4312019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4536155	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4935712	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4935727	0.82[JPT][hapmap]
rs7071603	0.82[JPT][hapmap]
rs7075289	0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7092014	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs715675	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7904833	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs920136	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs978588	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[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	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv948006	chr10:52127164-52177684	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52147000-52176600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:52157200-52177600	Weak transcription	Spleen	Spleen
3	chr10:52157800-52176800	Weak transcription	Lung	lung
4	chr10:52160800-52176800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr10:52163600-52176800	Weak transcription	Thymus	Thymus
6	chr10:52164400-52177600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:52164600-52176600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr10:52166600-52175800	Weak transcription	Primary T cells from cord blood	blood
9	chr10:52166600-52177400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr10:52166800-52177200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr10:52166800-52177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr10:52167000-52176800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr10:52167000-52176800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr10:52167000-52177200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr10:52167000-52177400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr10:52167600-52176800	Weak transcription	Primary B cells from cord blood	blood
17	chr10:52168000-52177400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:52168600-52176200	Weak transcription	Right Atrium	heart
19	chr10:52168600-52176600	Weak transcription	Fetal Brain Male	brain
20	chr10:52170200-52176400	Weak transcription	Small Intestine	intestine
21	chr10:52170200-52176800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr10:52170400-52176200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:52170400-52176800	Weak transcription	Right Ventricle	heart
24	chr10:52170400-52178400	Active TSS	GM12878-XiMat	blood
25	chr10:52170600-52176200	Weak transcription	HMEC	breast
26	chr10:52170600-52176600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr10:52170600-52176600	Weak transcription	NH-A	brain
28	chr10:52170600-52176800	Weak transcription	Aorta	Aorta
29	chr10:52170600-52177400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr10:52170600-52177400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr10:52170600-52177600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr10:52170800-52176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:52171400-52176000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr10:52171400-52176000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr10:52171400-52176800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr10:52171600-52176200	Weak transcription	HUVEC	blood vessel
37	chr10:52171600-52176200	Weak transcription	Osteobl	bone
38	chr10:52171800-52176800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr10:52172000-52176000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr10:52172200-52176800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr10:52172400-52176800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr10:52172400-52177400	Weak transcription	Gastric	stomach
43	chr10:52173200-52176800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr10:52173200-52176800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr10:52173400-52177400	Weak transcription	Fetal Intestine Large	intestine
46	chr10:52173600-52176800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr10:52173600-52177600	Weak transcription	Stomach Mucosa	stomach
48	chr10:52174200-52176000	Weak transcription	Brain Substantia Nigra	brain
49	chr10:52174200-52176800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr10:52174200-52177200	Weak transcription	Psoas Muscle	Psoas

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