Variant report

Variant	rs7257696
Chromosome Location	chr19:41128711-41128712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10403963	0.83[CHD][hapmap]
rs10405930	0.81[CHD][hapmap]
rs10410606	0.81[CHD][hapmap]
rs1131620	0.81[CHD][hapmap]
rs11670451	0.82[EUR][1000 genomes]
rs11671971	0.83[EUR][1000 genomes]
rs12610819	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes]
rs2162857	0.82[EUR][1000 genomes]
rs2278242	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2604902	0.81[CHD][hapmap]
rs28580028	0.81[EUR][1000 genomes]
rs3786529	0.89[EUR][1000 genomes]
rs56183542	0.81[EUR][1000 genomes]
rs7259067	0.83[CHD][hapmap]
rs7259237	0.83[CHD][hapmap]
rs7259554	0.83[CHD][hapmap]
rs7367	0.89[EUR][1000 genomes]
rs8107014	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
15	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
16	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
17	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7257696	PGLYRP1	cis	cerebellum	SCAN
rs7257696	CA11	cis	cerebellum	SCAN
rs7257696	CEACAM6	cis	cerebellum	SCAN
rs7257696	ZNF296	cis	cerebellum	SCAN
rs7257696	QPCTL	cis	cerebellum	SCAN
rs7257696	DMRTC2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41106000-41136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41116600-41137000	Weak transcription	Psoas Muscle	Psoas
3	chr19:41117000-41140200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:41120400-41139800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr19:41120600-41129400	Weak transcription	Pancreas	Pancrea
6	chr19:41120600-41133000	Weak transcription	Fetal Brain Male	brain
7	chr19:41120800-41139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:41120800-41140200	Weak transcription	Brain Anterior Caudate	brain
9	chr19:41121000-41129400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr19:41121200-41129400	Weak transcription	Right Atrium	heart
11	chr19:41121200-41136400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr19:41121200-41137400	Strong transcription	Fetal Muscle Leg	muscle
13	chr19:41121400-41132600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:41121400-41140200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr19:41121800-41129600	Weak transcription	HUVEC	blood vessel
16	chr19:41121800-41136800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:41122000-41130000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:41122000-41136800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:41122200-41129200	Strong transcription	Fetal Intestine Small	intestine
20	chr19:41122400-41129400	Strong transcription	Fetal Intestine Large	intestine
21	chr19:41122400-41129400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr19:41123000-41136800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr19:41123200-41129200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:41123200-41133400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:41123400-41140400	Weak transcription	Liver	Liver
26	chr19:41123800-41132600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:41124000-41129200	Weak transcription	Colon Smooth Muscle	Colon
28	chr19:41124000-41133400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:41124200-41133400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr19:41124200-41136600	Weak transcription	HSMMtube	muscle
31	chr19:41124400-41129000	Strong transcription	NHEK	skin
32	chr19:41124400-41133000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr19:41124400-41136000	Strong transcription	Ovary	ovary
34	chr19:41124800-41130200	Strong transcription	Osteobl	bone
35	chr19:41124800-41134000	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr19:41124800-41136000	Strong transcription	Adipose Nuclei	Adipose
37	chr19:41124800-41136200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr19:41125000-41128800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:41125000-41128800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:41125000-41129800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:41125000-41132800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:41125000-41135800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:41125200-41129000	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr19:41125200-41130000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:41125200-41130200	Strong transcription	Thymus	Thymus
46	chr19:41125200-41130400	Strong transcription	Primary T cells from cord blood	blood
47	chr19:41125200-41137200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:41125400-41129800	Strong transcription	Esophagus	oesophagus
49	chr19:41125800-41129200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr19:41125800-41136600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links