Variant report

Variant	rs17540338
Chromosome Location	chr15:52358533-52358534
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52310998..52313546-chr15:52356718..52359024,2	MCF-7	breast:
2	chr15:52351305..52354173-chr15:52357852..52359999,2	MCF-7	breast:
3	chr15:52347158..52349875-chr15:52357794..52360368,2	K562	blood:
4	chr15:52354567..52357172-chr15:52358028..52360343,2	K562	blood:

Variant related genes	Relation type
ENSG00000069956	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10152141	0.81[ASN][1000 genomes]
rs10518675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16964694	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16964700	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16964705	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16964720	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17612255	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17612326	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001741	0.81[ASN][1000 genomes]
rs2017967	0.85[ASN][1000 genomes]
rs2246726	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2306793	0.81[AMR][1000 genomes]
rs2414120	1.00[EUR][1000 genomes]
rs2414123	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2441779	1.00[EUR][1000 genomes]
rs2470593	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2470594	1.00[EUR][1000 genomes]
rs2470595	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2899484	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4375608	1.00[EUR][1000 genomes]
rs4456445	1.00[EUR][1000 genomes]
rs4491448	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774606	0.97[ASN][1000 genomes]
rs4775995	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs4775996	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4775997	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs55705935	0.97[ASN][1000 genomes]
rs55714716	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55873482	0.81[ASN][1000 genomes]
rs56307802	0.85[ASN][1000 genomes]
rs56677715	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58936667	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61546369	0.81[ASN][1000 genomes]
rs7177328	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs732097	0.89[CHB][hapmap]
rs74013638	0.81[ASN][1000 genomes]
rs74013640	0.81[ASN][1000 genomes]
rs74013641	0.81[ASN][1000 genomes]
rs74013642	0.81[ASN][1000 genomes]
rs74013644	0.85[ASN][1000 genomes]
rs74013645	0.85[ASN][1000 genomes]
rs74013646	0.85[ASN][1000 genomes]
rs74013647	0.85[ASN][1000 genomes]
rs74013648	0.85[ASN][1000 genomes]
rs74013653	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013654	0.85[ASN][1000 genomes]
rs74013656	0.92[ASN][1000 genomes]
rs74013657	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74013659	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013661	0.97[ASN][1000 genomes]
rs7497554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs751560	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033365	0.88[ASN][1000 genomes]
rs8033840	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8036048	0.90[ASN][1000 genomes]
rs8041281	1.00[EUR][1000 genomes]
rs9796534	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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 target site	23 gene(s)	inside rSNPs	diseases
4	nsv984071	chr15:52356234-52359266	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1039841	chr15:52357448-52381377	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr15:52314400-52359800	Weak transcription	Fetal Brain Male	brain
2	chr15:52332600-52361800	Weak transcription	Gastric	stomach
3	chr15:52334000-52361400	Weak transcription	Small Intestine	intestine
4	chr15:52337600-52360600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:52339400-52359200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:52340200-52362200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:52343000-52359400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:52344600-52362000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:52345000-52358600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:52345600-52358800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:52345600-52358800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:52345800-52359200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:52346200-52359000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:52347200-52358800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:52347600-52358800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:52347800-52358800	Strong transcription	HSMM	muscle
17	chr15:52348000-52361200	Weak transcription	Stomach Mucosa	stomach
18	chr15:52348200-52358600	Strong transcription	Primary B cells from cord blood	blood
19	chr15:52348400-52358800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:52348400-52359200	Strong transcription	NHDF-Ad	bronchial
21	chr15:52350800-52358600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:52352200-52359200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:52352200-52361400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:52352200-52363600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:52352800-52358800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:52352800-52359800	Weak transcription	Colonic Mucosa	Colon
27	chr15:52353000-52360000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:52353000-52361800	Weak transcription	Pancreas	Pancrea
29	chr15:52353000-52362200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:52353200-52360400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:52353200-52370800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:52353600-52368800	Weak transcription	HSMMtube	muscle
33	chr15:52355600-52358800	Weak transcription	Fetal Stomach	stomach
34	chr15:52355600-52359800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:52355600-52361600	Weak transcription	Fetal Intestine Small	intestine
36	chr15:52355600-52363400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:52355800-52358600	Weak transcription	Thymus	Thymus
38	chr15:52356000-52359000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:52356000-52359000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:52356000-52363200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:52356200-52358600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:52356200-52358600	Weak transcription	Colon Smooth Muscle	Colon
43	chr15:52356200-52358600	Weak transcription	NHLF	lung
44	chr15:52356200-52358800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:52356200-52359200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr15:52356200-52359200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:52356200-52359200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:52356200-52359400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:52356200-52359600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:52356200-52359800	Weak transcription	Primary hematopoietic stem cells	blood

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