Variant report

Variant	rs2941505
Chromosome Location	chr17:37832704-37832705
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37827266..37833048-chr17:37842420..37846685,6	MCF-7	breast:
2	chr17:37831185..37834082-chr17:37834378..37836489,3	MCF-7	breast:
3	chr17:37832659..37835422-chr17:37879679..37882174,3	K562	blood:
4	chr17:37793727..37796192-chr17:37829753..37832726,2	MCF-7	breast:
5	chr17:37829760..37835390-chr17:37853762..37858979,8	MCF-7	breast:
6	chr17:37806036..37809512-chr17:37829090..37833058,4	K562	blood:
7	chr17:37832364..37833972-chr17:37842074..37844031,2	K562	blood:
8	chr17:37831092..37832892-chr17:37842525..37844810,2	MCF-7	breast:
9	chr17:37830304..37832769-chr17:37860083..37864558,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000141736	Chromatin interaction
ENSG00000161395	Chromatin interaction
ENSG00000131748	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1018246	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1053651	0.86[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs10852934	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11651497	0.87[ASN][1000 genomes]
rs11658786	0.92[ASN][1000 genomes]
rs11869286	0.86[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs12150298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs14050	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1476278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495099	0.88[ASN][1000 genomes]
rs1495100	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495101	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495102	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565920	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565923	0.82[CEU][hapmap]
rs1810132	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs1874228	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1877031	0.86[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2247862	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271308	0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2271309	0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2313171	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517952	0.91[ASN][1000 genomes]
rs2517953	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517954	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517955	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517956	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517958	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517959	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517960	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2934951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934952	0.90[CEU][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934953	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934956	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934971	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs2941503	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941504	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952151	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952152	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952155	0.88[CHB][hapmap]
rs2952156	0.82[CEU][hapmap]
rs33953566	0.87[ASN][1000 genomes]
rs35734596	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3751903	0.88[ASN][1000 genomes]
rs3764352	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs3764353	0.87[ASN][1000 genomes]
rs3794712	0.84[ASN][1000 genomes]
rs3817160	0.88[ASN][1000 genomes]
rs407307	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4794817	0.88[ASN][1000 genomes]
rs4795388	0.82[ASN][1000 genomes]
rs4795389	0.86[ASN][1000 genomes]
rs4795390	0.87[ASN][1000 genomes]
rs732083	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732084	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077172	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879606	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs881844	0.83[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs903501	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903502	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907087	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907088	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907090	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907094	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs9303274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931992	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs9675194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915323	0.80[ASN][1000 genomes]
rs9972882	0.86[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv516757	chr17:37781849-37834541	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
8	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
9	nsv908213	chr17:37807698-37839493	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
10	nsv528093	chr17:37814080-37866005	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv908214	chr17:37814224-37861833	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv908215	chr17:37818561-37834541	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
13	esv1848656	chr17:37830900-37834998	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2941505	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs2941505	PGAP3	cis	Heart Left Ventricle	GTEx
rs2941505	PGAP3	cis	Muscle Skeletal	GTEx
rs2941505	PGAP3	cis	Thyroid	GTEx
rs2941505	PGAP3	cis	Skin Sun Exposed Lower leg	GTEx
rs2941505	GSDML	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37824800-37833200	Enhancers	Fetal Heart	heart
2	chr17:37825200-37833000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr17:37825800-37833000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:37826400-37833000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:37827600-37832800	Enhancers	Fetal Intestine Large	intestine
6	chr17:37827800-37837800	Genic enhancers	Fetal Intestine Small	intestine
7	chr17:37828400-37834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:37828400-37834200	Weak transcription	Fetal Kidney	kidney
9	chr17:37828600-37833000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr17:37828600-37833200	Weak transcription	Brain Anterior Caudate	brain
11	chr17:37828600-37834200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr17:37828600-37836000	Weak transcription	Ovary	ovary
13	chr17:37828600-37843200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr17:37828800-37835400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:37828800-37839800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:37829000-37839600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr17:37829000-37839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr17:37829200-37833000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:37829400-37834000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:37829400-37837400	Enhancers	Primary B cells from cord blood	blood
21	chr17:37829600-37835600	Weak transcription	Brain Germinal Matrix	brain
22	chr17:37829600-37837600	Enhancers	Primary B cells from peripheral blood	blood
23	chr17:37829800-37833000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:37829800-37833800	Enhancers	Right Ventricle	heart
25	chr17:37829800-37834000	Strong transcription	Fetal Stomach	stomach
26	chr17:37829800-37835000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr17:37829800-37843600	Weak transcription	NHDF-Ad	bronchial
28	chr17:37830200-37836800	Enhancers	Stomach Mucosa	stomach
29	chr17:37830400-37834200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr17:37830400-37839400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr17:37830600-37832800	Enhancers	Pancreas	Pancrea
32	chr17:37830600-37833600	Enhancers	Esophagus	oesophagus
33	chr17:37830600-37834600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr17:37830600-37835200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr17:37830600-37837000	Enhancers	Fetal Thymus	thymus
36	chr17:37830600-37837200	Enhancers	Duodenum Mucosa	Duodenum
37	chr17:37830600-37837400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr17:37830800-37832800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr17:37830800-37835600	Enhancers	Primary T cells fromperipheralblood	blood
40	chr17:37830800-37837000	Enhancers	Left Ventricle	heart
41	chr17:37830800-37837600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr17:37830800-37838000	Enhancers	GM12878-XiMat	blood
43	chr17:37831000-37833000	Enhancers	HSMM	muscle
44	chr17:37831000-37835200	Enhancers	A549	lung
45	chr17:37831000-37836000	Enhancers	HSMMtube	muscle
46	chr17:37831000-37836400	Enhancers	Psoas Muscle	Psoas
47	chr17:37831000-37837600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr17:37831200-37832800	Enhancers	Brain Hippocampus Middle	brain
49	chr17:37831200-37833200	Enhancers	Stomach Smooth Muscle	stomach
50	chr17:37831200-37833600	Enhancers	Sigmoid Colon	Sigmoid Colon

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