Variant report

Variant	rs2952156
Chromosome Location	chr17:37876835-37876836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:37856670..37858872-chr17:37874487..37877508,3	MCF-7	breast:
2	chr17:37858390..37860926-chr17:37875652..37877494,2	K562	blood:
3	chr17:37875103..37877735-chr17:37878952..37881487,4	K562	blood:
4	chr17:37870758..37873083-chr17:37874555..37877273,2	K562	blood:
5	chr17:37875233..37878023-chr17:37910337..37912992,2	MCF-7	breast:
6	chr17:37843958..37845642-chr17:37874066..37877258,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141736	Chromatin interaction
ENSG00000161395	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1058808	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11653998	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150298	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs12150603	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs12940986	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs14050	0.90[CEU][hapmap]
rs1476278	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs1565922	0.82[CHB][hapmap]
rs1565923	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1810132	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2088126	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247862	0.90[CEU][hapmap];0.83[YRI][hapmap]
rs2313171	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs2517951	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517954	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs2517955	0.86[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2517956	0.95[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap]
rs2517957	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs2517958	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs2643194	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2643195	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2904766	0.80[ASN][1000 genomes]
rs2934952	0.95[CEU][hapmap]
rs2934953	0.90[CEU][hapmap];0.80[JPT][hapmap]
rs2934967	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934971	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2941503	0.95[CEU][hapmap]
rs2941504	0.90[CEU][hapmap];0.86[YRI][hapmap]
rs2941505	0.82[CEU][hapmap]
rs2941506	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs2941520	0.88[EUR][1000 genomes]
rs2952151	0.90[CEU][hapmap]
rs2952155	0.92[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs2952157	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4252627	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795393	0.83[ASN][1000 genomes]
rs8078228	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs903501	0.90[CEU][hapmap];0.82[CHB][hapmap];0.80[YRI][hapmap]
rs903502	0.81[CEU][hapmap]
rs903506	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907087	0.90[CEU][hapmap]
rs907089	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs9303274	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs9675194	0.81[CEU][hapmap];0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1056234	chr17:37862605-37909988	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv908216	chr17:37863015-37879588	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv908217	chr17:37863708-37879588	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv574993	chr17:37866135-37880978	Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv908218	chr17:37866591-37879588	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv1829991	chr17:37869192-37876898	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2952156	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs2952156	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs2952156	PGAP3	cis	Thyroid	GTEx
rs2952156	PGAP3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37858000-37885200	Weak transcription	Fetal Brain Male	brain
2	chr17:37858000-37885600	Weak transcription	Hela-S3	cervix
3	chr17:37858200-37882600	Weak transcription	NHDF-Ad	bronchial
4	chr17:37858400-37879600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:37859400-37881000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr17:37861400-37883600	Weak transcription	Brain Substantia Nigra	brain
7	chr17:37862200-37877000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
8	chr17:37862200-37885200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr17:37862400-37877600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:37862400-37878800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:37862400-37885400	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr17:37862400-37885600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:37862400-37885600	Strong transcription	Fetal Stomach	stomach
14	chr17:37862400-37885800	Weak transcription	Right Atrium	heart
15	chr17:37862600-37885600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr17:37862800-37878800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:37862800-37883200	Weak transcription	Small Intestine	intestine
18	chr17:37862800-37885600	Strong transcription	Fetal Intestine Large	intestine
19	chr17:37863000-37877000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr17:37863000-37878800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr17:37863000-37879000	Strong transcription	HSMMtube	muscle
22	chr17:37863000-37879600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr17:37863000-37885600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:37863200-37879400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr17:37863200-37885600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr17:37863200-37885800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:37863600-37883000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:37863600-37885600	Strong transcription	Fetal Intestine Small	intestine
29	chr17:37863800-37881000	Weak transcription	Thymus	Thymus
30	chr17:37863800-37881200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr17:37864600-37882200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:37864800-37883400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:37865000-37884800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr17:37865800-37884200	Weak transcription	Brain Angular Gyrus	brain
35	chr17:37866000-37885000	Weak transcription	Primary B cells from cord blood	blood
36	chr17:37866200-37879400	Strong transcription	Placenta	Placenta
37	chr17:37866600-37879600	Weak transcription	Fetal Brain Female	brain
38	chr17:37867000-37882800	Weak transcription	Fetal Thymus	thymus
39	chr17:37868400-37882800	Weak transcription	Brain Anterior Caudate	brain
40	chr17:37869200-37883000	Weak transcription	Brain Hippocampus Middle	brain
41	chr17:37870400-37878600	Strong transcription	Fetal Lung	lung
42	chr17:37871400-37877000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr17:37872200-37886000	Weak transcription	NH-A	brain
44	chr17:37872400-37878600	Weak transcription	Fetal Kidney	kidney
45	chr17:37872400-37881000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr17:37872600-37880800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr17:37872600-37881000	Weak transcription	Spleen	Spleen
48	chr17:37872800-37881000	Weak transcription	Brain Germinal Matrix	brain
49	chr17:37872800-37885400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr17:37873000-37879400	Weak transcription	HUVEC	blood vessel

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