Variant report

Variant	rs2965186
Chromosome Location	chr19:19497195-19497196
allele	G/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19494550..19497983-chr19:19513188..19518336,8	MCF-7	breast:
2	chr19:19496697..19498287-chr19:19583016..19585062,2	MCF-7	breast:
3	chr19:18390819..18392505-chr19:19495105..19497896,2	K562	blood:
4	chr17:2240537..2241373-chr19:19496561..19497247,2	Hela-S3	cervix:
5	chr19:19494732..19500297-chr19:19512585..19520288,14	MCF-7	breast:
6	chr19:19491673..19504307-chr19:19513999..19523684,33	K562	blood:
7	chr19:19494923..19497823-chr19:19573798..19576950,3	K562	blood:
8	chr19:19303809..19306527-chr19:19495529..19497596,2	K562	blood:
9	chr19:19303122..19305309-chr19:19496096..19498095,2	K562	blood:
10	chr19:19496792..19497635-chr5:177631182..177631713,2	Hela-S3	cervix:
11	chr12:51157187..51158117-chr19:19496545..19497370,2	NB4	blood:
12	chr19:19496290..19497914-chr19:19774313..19776411,2	MCF-7	breast:
13	chr19:19492268..19501550-chr19:19512499..19523684,29	K562	blood:
14	chr19:19496705..19497560-chr3:23958156..23958868,2	NB4	blood:

No data

Variant related genes	Relation type
ENSG00000141258	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000167721	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000267234	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000167491	Chromatin interaction
ENSG00000254901	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10406278	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10423874	0.85[CEU][hapmap]
rs1064395	0.96[TSI][hapmap]
rs11085264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs11555053	1.00[TSI][hapmap]
rs11668203	0.91[EUR][1000 genomes]
rs11669730	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs11670687	0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs11670761	0.81[EUR][1000 genomes]
rs11670775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs11670882	0.93[CEU][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs11671253	0.84[EUR][1000 genomes]
rs1529745	0.89[EUR][1000 genomes]
rs1557723	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1560687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17216041	0.89[MEX][hapmap];1.00[TSI][hapmap]
rs17684164	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs17751061	0.86[CEU][hapmap];1.00[TSI][hapmap]
rs1989867	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2010506	0.85[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs2011503	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2060274	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2315282	0.81[EUR][1000 genomes]
rs2860494	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2905429	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905433	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905434	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2916070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2916072	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2916075	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2965178	0.86[EUR][1000 genomes]
rs2965179	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965181	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2965187	0.84[AFR][1000 genomes]
rs2965190	0.82[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2965195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2965201	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34487417	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34667451	0.84[EUR][1000 genomes]
rs4239639	0.80[AMR][1000 genomes]
rs45556231	0.81[EUR][1000 genomes]
rs45631651	0.81[EUR][1000 genomes]
rs4808204	0.84[EUR][1000 genomes]
rs4808205	0.81[EUR][1000 genomes]
rs4808206	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4808934	0.96[TSI][hapmap]
rs4808951	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4808958	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4808968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs4808969	0.81[EUR][1000 genomes]
rs55927782	0.81[EUR][1000 genomes]
rs56280531	0.84[EUR][1000 genomes]
rs56291054	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56330647	0.82[EUR][1000 genomes]
rs58074958	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6511027	0.96[TSI][hapmap]
rs6511029	0.84[EUR][1000 genomes]
rs7245689	0.82[EUR][1000 genomes]
rs7250233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs7252453	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs7256028	0.82[EUR][1000 genomes]
rs751857	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs754256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs756999	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8100927	0.81[EUR][1000 genomes]
rs8101219	0.91[ASW][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs8102502	0.93[CEU][hapmap];0.96[TSI][hapmap]
rs8105642	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8111093	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs998732	0.89[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2965186	IL12RB1	cis	parietal	SCAN
rs2965186	OCEL1	cis	parietal	SCAN
rs2965186	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs2965186	DDX49	cis	cerebellum	SCAN
rs2965186	JUND	cis	parietal	SCAN
rs2965186	GATAD2A	cis	parietal	SCAN
rs2965186	LSM4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19495200-19497200	Active TSS	Fetal Brain Female	brain
2	chr19:19495200-19497600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:19495400-19497800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr19:19495400-19498200	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:19495400-19498400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:19495600-19497200	Active TSS	Psoas Muscle	Psoas
7	chr19:19495600-19497200	Active TSS	Right Ventricle	heart
8	chr19:19495600-19497400	Active TSS	Brain Angular Gyrus	brain
9	chr19:19495600-19497400	Active TSS	HSMMtube	muscle
10	chr19:19495600-19497600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:19495600-19497600	Active TSS	Ovary	ovary
12	chr19:19495600-19497600	Active TSS	Small Intestine	intestine
13	chr19:19495600-19497800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr19:19495600-19497800	Active TSS	HSMM	muscle
15	chr19:19495600-19498000	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr19:19495600-19498000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr19:19495800-19497200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:19495800-19497200	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr19:19495800-19497200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:19495800-19497200	Active TSS	Brain Anterior Caudate	brain
21	chr19:19495800-19497200	Active TSS	Brain Hippocampus Middle	brain
22	chr19:19495800-19497200	Active TSS	Brain Substantia Nigra	brain
23	chr19:19495800-19497200	Active TSS	Colon Smooth Muscle	Colon
24	chr19:19495800-19497200	Active TSS	Esophagus	oesophagus
25	chr19:19495800-19497400	Active TSS	H1 Cell Line	embryonic stem cell
26	chr19:19495800-19497400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:19495800-19497400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr19:19495800-19497400	Active TSS	Gastric	stomach
29	chr19:19495800-19497400	Active TSS	Pancreas	Pancrea
30	chr19:19495800-19497400	Active TSS	NHLF	lung
31	chr19:19495800-19497600	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr19:19495800-19497600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:19495800-19497600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:19495800-19497600	Active TSS	Left Ventricle	heart
35	chr19:19495800-19497600	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr19:19495800-19497600	Active TSS	A549	lung
37	chr19:19495800-19497800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:19495800-19497800	Active TSS	Aorta	Aorta
39	chr19:19495800-19497800	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr19:19495800-19497800	Active TSS	Fetal Kidney	kidney
41	chr19:19495800-19497800	Active TSS	Placenta Amnion	Placenta Amnion
42	chr19:19495800-19498000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:19495800-19498000	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr19:19496000-19497200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr19:19496000-19497200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:19496000-19497200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:19496000-19497200	Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr19:19496000-19497200	Active TSS	Primary T cells from cord blood	blood
49	chr19:19496000-19497200	Active TSS	Primary T cells fromperipheralblood	blood
50	chr19:19496000-19497200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links