Variant report

Variant	rs538649
Chromosome Location	chr19:37412887-37412888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37405380..37408333-chr19:37412047..37415045,3	MCF-7	breast:
2	chr19:37411760..37413673-chr19:37428843..37431824,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185869	Chromatin interaction
ENSG00000198453	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1227564	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1363751	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1363753	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1375476	0.81[ASW][hapmap];0.85[CEU][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs1375477	0.81[EUR][1000 genomes]
rs1612652	0.82[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap]
rs1623796	0.86[CEU][hapmap];0.93[JPT][hapmap]
rs1624087	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1625963	0.85[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs1626675	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1643418	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1644634	0.85[ASW][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs1644637	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1644647	0.85[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1644650	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1644651	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1644652	0.81[EUR][1000 genomes]
rs1644662	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1644669	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1644672	0.82[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap]
rs1644673	0.82[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap]
rs1667330	0.84[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1667333	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1667335	0.85[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs1667336	0.81[EUR][1000 genomes]
rs1667337	0.81[EUR][1000 genomes]
rs1667341	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1667351	0.82[JPT][hapmap]
rs1667353	0.82[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap]
rs1667354	0.82[EUR][1000 genomes]
rs1667382	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1667383	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385374	0.83[TSI][hapmap]
rs2547054	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2551062	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2595545	0.82[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap]
rs4254428	0.83[TSI][hapmap]
rs4806407	0.83[TSI][hapmap]
rs496730	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs497130	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs500126	0.84[AFR][1000 genomes]
rs520288	0.85[EUR][1000 genomes]
rs523979	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs524933	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs533863	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs538534	1.00[CEU][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes]
rs540472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541966	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs542729	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs543212	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs543518	0.82[JPT][hapmap]
rs543609	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs544964	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs548077	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs560480	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs560541	0.84[AFR][1000 genomes]
rs571294	0.92[LWK][hapmap];0.87[MEX][hapmap]
rs578977	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs580846	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6510588	0.80[TSI][hapmap]
rs7245882	0.83[TSI][hapmap]
rs7258360	0.83[TSI][hapmap]
rs7259605	0.85[EUR][1000 genomes]
rs8109501	0.83[TSI][hapmap]
rs826263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs826285	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826295	0.87[EUR][1000 genomes]
rs826298	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs826305	0.85[ASW][hapmap];0.92[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs826306	0.85[AFR][1000 genomes]
rs826320	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs860392	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
13	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
16	nsv458569	chr19:37331614-37412887	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv579462	chr19:37331614-37412887	Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	nsv523848	chr19:37357289-37487632	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs538649	CAPN12	cis	cerebellum	SCAN
rs538649	ZNF420	cis	lymphoblastoid	seeQTL
rs538649	ZNF585B	cis	Artery Tibial	GTEx
rs538649	PSMC4	cis	parietal	SCAN
rs538649	AC012309.5	cis	Thyroid	GTEx
rs538649	CEACAM4	cis	parietal	SCAN
rs538649	ZNF607	cis	parietal	SCAN
rs538649	ZNF540	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37408200-37413000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:37408200-37413000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:37408200-37413000	Weak transcription	Aorta	Aorta
4	chr19:37408200-37413000	Weak transcription	Colonic Mucosa	Colon
5	chr19:37408200-37436400	Weak transcription	Fetal Thymus	thymus
6	chr19:37408200-37440600	Weak transcription	Stomach Mucosa	stomach
7	chr19:37408400-37413000	Weak transcription	Fetal Intestine Large	intestine
8	chr19:37408400-37413000	Weak transcription	Spleen	Spleen
9	chr19:37408400-37417000	Weak transcription	Fetal Kidney	kidney
10	chr19:37408400-37440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:37408600-37439600	Weak transcription	Fetal Heart	heart
12	chr19:37408800-37414800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr19:37408800-37415200	Strong transcription	Left Ventricle	heart
14	chr19:37409000-37413800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:37409000-37413800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:37409000-37413800	Strong transcription	Fetal Muscle Leg	muscle
17	chr19:37409000-37414200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:37409000-37414800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:37409000-37415000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:37409000-37444800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:37409000-37447400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:37409200-37413000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr19:37409200-37413800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr19:37409200-37413800	Strong transcription	Brain Anterior Caudate	brain
25	chr19:37409200-37414200	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr19:37409200-37414400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:37409200-37414600	Strong transcription	Fetal Lung	lung
28	chr19:37409200-37415000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:37409400-37413800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:37409400-37414000	Strong transcription	Fetal Brain Female	brain
31	chr19:37409400-37414800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr19:37409400-37415000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:37409600-37423600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:37409800-37413800	Strong transcription	Dnd41	blood
35	chr19:37409800-37416000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:37409800-37421400	Weak transcription	Fetal Brain Male	brain
37	chr19:37410000-37413000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr19:37410000-37415400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:37410200-37413800	Strong transcription	Fetal Stomach	stomach
40	chr19:37410200-37415000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:37410600-37413000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:37410600-37413000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:37410600-37413000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:37410600-37413000	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:37410600-37413000	Weak transcription	Esophagus	oesophagus
46	chr19:37410600-37413000	Weak transcription	Gastric	stomach
47	chr19:37410600-37413000	Weak transcription	Pancreas	Pancrea
48	chr19:37410600-37413000	Weak transcription	Right Ventricle	heart
49	chr19:37410600-37413200	Weak transcription	HSMMtube	muscle
50	chr19:37410600-37413400	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links