Variant report

Variant	rs3750014
Chromosome Location	chr7:4815603-4815604
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:4721460..4723337-chr7:4813356..4816619,3	MCF-7	breast:
2	chr7:4815302..4817443-chr7:4835837..4838194,2	MCF-7	breast:
3	chr7:4813279..4817996-chr7:4818432..4827499,15	MCF-7	breast:
4	chr7:4777828..4782067-chr7:4812094..4815733,5	K562	blood:
5	chr7:4779354..4780876-chr7:4813776..4815968,2	K562	blood:
6	chr7:4720968..4723057-chr7:4814172..4816062,2	MCF-7	breast:
7	chr7:4723905..4726708-chr7:4815348..4817182,2	K562	blood:
8	chr7:4815353..4817520-chr7:4819712..4821919,3	K562	blood:
9	chr2:27434760..27435750-chr7:4814658..4815639,2	Hela-S3	cervix:
10	chr7:4815133..4816843-chr7:4827652..4829770,2	MCF-7	breast:
11	chr4:139162554..139163537-chr7:4815075..4815798,2	NB4	blood:
12	chr7:4796791..4799856-chr7:4814075..4815841,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000242802	Chromatin interaction
ENSG00000164916	Chromatin interaction
ENSG00000151012	Chromatin interaction
ENSG00000264474	Chromatin interaction
ENSG00000138074	Chromatin interaction
ENSG00000138085	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10232558	1.00[CHB][hapmap]
rs10270796	1.00[CHB][hapmap]
rs11628	0.94[ASW][hapmap];0.85[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11764272	0.83[ASN][1000 genomes]
rs11764275	0.83[ASN][1000 genomes]
rs11768079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11772411	0.83[ASN][1000 genomes]
rs12701943	0.83[ASN][1000 genomes]
rs13224156	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13236366	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17135096	0.85[CEU][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17135099	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17135102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135110	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17135115	0.81[CHD][hapmap]
rs17135121	0.83[ASN][1000 genomes]
rs17135128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17829969	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs2011679	1.00[CHB][hapmap]
rs34217589	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35713835	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3750012	1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs3750013	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3750015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750016	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3750018	0.81[ASN][1000 genomes]
rs3750019	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801041	0.96[ASN][1000 genomes]
rs3816852	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs59174566	0.83[ASN][1000 genomes]
rs60972000	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958952	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963791	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs6975325	0.93[ASN][1000 genomes]
rs73671922	0.83[ASN][1000 genomes]
rs749404	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7777890	0.85[CEU][hapmap]
rs7801122	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7803727	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs879217	1.00[CHB][hapmap];0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv887377	chr7:4730535-4862259	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv887378	chr7:4730535-4929721	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv887379	chr7:4749527-4828593	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv887380	chr7:4760124-4929721	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv471293	chr7:4764861-4885221	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv887381	chr7:4769030-4880954	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv823994	chr7:4792385-4928328	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv887382	chr7:4792762-4880954	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv8033	chr7:4802287-5086597	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	nsv1022678	chr7:4810626-5113387	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
15	nsv538705	chr7:4810626-5113387	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
16	nsv482101	chr7:4815264-4831397	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3750014	KDELR2	cis	cerebellum	SCAN
rs3750014	FOXK1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4813800-4817000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:4814000-4816200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr7:4814000-4816400	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr7:4814200-4816000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr7:4814200-4816200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr7:4814200-4816200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr7:4814200-4816200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr7:4814200-4816200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr7:4814200-4816400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:4814400-4815800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:4814400-4815800	Active TSS	Aorta	Aorta
12	chr7:4814400-4816000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr7:4814400-4816000	Active TSS	Ovary	ovary
14	chr7:4814400-4816200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr7:4814400-4816200	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr7:4814400-4816200	Active TSS	Psoas Muscle	Psoas
17	chr7:4814400-4816400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:4814400-4816400	Active TSS	Fetal Kidney	kidney
19	chr7:4814400-4816400	Active TSS	GM12878-XiMat	blood
20	chr7:4814400-4816400	Active TSS	Osteobl	bone
21	chr7:4814400-4816600	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr7:4814600-4815800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:4814600-4815800	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr7:4814600-4815800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:4814600-4815800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:4814600-4815800	Active TSS	Brain Cingulate Gyrus	brain
27	chr7:4814600-4815800	Active TSS	Brain Hippocampus Middle	brain
28	chr7:4814600-4815800	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr7:4814600-4815800	Active TSS	Colon Smooth Muscle	Colon
30	chr7:4814600-4815800	Active TSS	Duodenum Mucosa	Duodenum
31	chr7:4814600-4815800	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr7:4814600-4815800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr7:4814600-4815800	Active TSS	Fetal Brain Female	brain
34	chr7:4814600-4815800	Active TSS	Fetal Heart	heart
35	chr7:4814600-4815800	Active TSS	Fetal Lung	lung
36	chr7:4814600-4815800	Active TSS	Fetal Stomach	stomach
37	chr7:4814600-4815800	Active TSS	Stomach Mucosa	stomach
38	chr7:4814600-4815800	Active TSS	Spleen	Spleen
39	chr7:4814600-4815800	Active TSS	Hela-S3	cervix
40	chr7:4814600-4815800	Active TSS	HUVEC	blood vessel
41	chr7:4814600-4815800	Active TSS	K562	blood
42	chr7:4814600-4815800	Active TSS	Monocytes-CD14+_RO01746	blood
43	chr7:4814600-4816000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr7:4814600-4816000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:4814600-4816000	Active TSS	Lung	lung
46	chr7:4814600-4816000	Active TSS	Placenta Amnion	Placenta Amnion
47	chr7:4814600-4816000	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr7:4814600-4816000	Active TSS	Small Intestine	intestine
49	chr7:4814600-4816000	Bivalent/Poised TSS	HepG2	liver
50	chr7:4814600-4816200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links