Variant report

Variant	rs2965201
Chromosome Location	chr19:19478051-19478052
allele	C/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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19477404..19478255-chr19:19599787..19600745,2	K562	blood:
2	chr19:19475560..19479223-chr19:19494515..19497733,3	K562	blood:
3	chr19:19475956..19479022-chr19:19487056..19489762,4	MCF-7	breast:
4	chr19:19477286..19479329-chr19:19514335..19517892,4	MCF-7	breast:
5	chr19:19464713..19466324-chr19:19477135..19479522,2	K562	blood:
6	chr19:19476462..19478976-chr19:19482373..19484505,3	K562	blood:
7	chr19:19475888..19481380-chr19:19598435..19602231,6	MCF-7	breast:
8	chr19:19477732..19478297-chr19:19517505..19518349,2	K562	blood:
9	chr19:19477369..19478572-chr19:19517483..19518545,4	MCF-7	breast:
10	chr19:19476063..19479194-chr19:19516845..19521061,4	K562	blood:
11	chr19:19476417..19478794-chr19:19498125..19500397,2	K562	blood:
12	chr19:19476043..19479075-chr19:19495694..19499474,5	MCF-7	breast:
13	chr19:19475761..19480142-chr19:19495038..19498469,6	MCF-7	breast:
14	chr19:19475560..19478131-chr19:19494515..19496869,2	K562	blood:
15	chr19:19477200..19478311-chr19:19600704..19601856,7	MCF-7	breast:
16	chr19:19469711..19473651-chr19:19475756..19478808,4	K562	blood:
17	chr19:19477386..19478234-chr19:19517375..19518109,3	MCF-7	breast:
18	chr19:19477390..19478315-chr19:19586432..19586933,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction
ENSG00000129933	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10406278	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10407933	0.81[CEU][hapmap]
rs10423874	0.87[CEU][hapmap]
rs1064395	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs11085264	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs11555053	0.81[CEU][hapmap];1.00[TSI][hapmap]
rs11668203	0.85[EUR][1000 genomes]
rs11669730	0.80[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs11670687	0.89[YRI][hapmap]
rs11670775	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs11670882	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs1529745	0.83[EUR][1000 genomes]
rs1557723	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1560687	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];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17216041	0.81[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs17684164	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs17751061	0.87[CEU][hapmap];1.00[TSI][hapmap]
rs1989867	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2010506	0.88[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs2011503	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2060274	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2315023	0.82[AMR][1000 genomes]
rs2315282	0.86[EUR][1000 genomes]
rs2860494	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2905429	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2905433	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2905434	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2916070	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];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2916072	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2916075	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2965178	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965179	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965181	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965184	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];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2965186	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]
rs2965187	0.88[AFR][1000 genomes]
rs2965190	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2965195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2965202	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34487417	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4239639	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4808206	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap]
rs4808934	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs4808944	0.82[AMR][1000 genomes]
rs4808951	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4808958	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4808968	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs56280531	0.81[AFR][1000 genomes]
rs56291054	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57436187	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58074958	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6511027	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs6511029	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7250233	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap]
rs7252453	0.94[CEU][hapmap]
rs751857	0.81[ASW][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap]
rs754256	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];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs756999	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8101219	0.96[GIH][hapmap];0.84[YRI][hapmap]
rs8102502	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs8105642	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8111093	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs998732	0.81[CEU][hapmap];0.89[MEX][hapmap];0.82[MKK][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
rs2965201	JUND	cis	parietal	SCAN
rs2965201	LSM4	cis	cerebellum	SCAN
rs2965201	IL12RB1	cis	parietal	SCAN
rs2965201	GATAD2A	cis	parietal	SCAN
rs2965201	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs2965201	OCEL1	cis	parietal	SCAN
rs2965201	DDX49	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19465200-19483600	Weak transcription	NH-A	brain
2	chr19:19469400-19482000	Weak transcription	Esophagus	oesophagus
3	chr19:19469800-19488400	Weak transcription	Gastric	stomach
4	chr19:19475800-19488000	Weak transcription	Small Intestine	intestine
5	chr19:19476000-19478200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:19476000-19478200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:19476000-19481800	Weak transcription	NHEK	skin
8	chr19:19476200-19478200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr19:19476200-19478200	Enhancers	Placenta	Placenta
10	chr19:19476200-19482000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:19476200-19482000	Weak transcription	HUVEC	blood vessel
12	chr19:19476200-19483200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:19476200-19483600	Weak transcription	Fetal Intestine Large	intestine
14	chr19:19476200-19483600	Weak transcription	NHLF	lung
15	chr19:19476200-19483800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:19476200-19488200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:19476200-19488400	Weak transcription	Right Atrium	heart
18	chr19:19477000-19478200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr19:19477400-19478200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:19477400-19478800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:19477600-19478200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:19477600-19478200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:19477800-19478200	Enhancers	Hela-S3	cervix
24	chr19:19477800-19478200	Enhancers	K562	blood
25	chr19:19477800-19478400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr19:19477800-19478800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:19477800-19479400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:19477800-19479600	Weak transcription	Fetal Intestine Small	intestine
29	chr19:19477800-19481600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:19477800-19481800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:19477800-19481800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr19:19477800-19481800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:19477800-19481800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr19:19477800-19481800	Weak transcription	HSMM	muscle
35	chr19:19477800-19482000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr19:19477800-19482000	Weak transcription	HMEC	breast
37	chr19:19477800-19482800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr19:19477800-19483000	Weak transcription	Primary B cells from cord blood	blood
39	chr19:19477800-19483000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:19477800-19483200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr19:19477800-19483200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr19:19477800-19483200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr19:19477800-19483200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:19477800-19483600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:19477800-19483600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:19477800-19483600	Weak transcription	Brain Hippocampus Middle	brain
47	chr19:19477800-19483600	Weak transcription	NHDF-Ad	bronchial
48	chr19:19477800-19488400	Weak transcription	Fetal Muscle Leg	muscle
49	chr19:19477800-19488600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:19477800-19488600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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