Variant report

Variant	rs2304186
Chromosome Location	chr19:40739721-40739722
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40736321..40741961-chr19:40743077..40747922,9	K562	blood:
2	chr19:40736720..40741002-chr19:40742937..40745961,5	K562	blood:
3	chr19:40730620..40735723-chr19:40738673..40743679,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105219	Chromatin interaction
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11083554	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12151335	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs12459567	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12460555	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12609014	0.85[ASN][1000 genomes]
rs12977474	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12985477	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16974196	0.82[JPT][hapmap]
rs2368575	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs33933140	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34894858	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.86[ASN][1000 genomes]
rs35562135	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3745195	0.91[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap]
rs3746006	0.81[JPT][hapmap]
rs4479364	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4490097	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs4502340	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap]
rs4802072	0.82[AMR][1000 genomes]
rs4802076	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4803324	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803325	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803326	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55710849	0.82[ASN][1000 genomes]
rs57158010	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58502633	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67322193	0.86[ASN][1000 genomes]
rs7259541	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7507651	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs8110323	0.85[ASN][1000 genomes]
rs890773	0.91[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs892117	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1062755	chr19:40737463-40758235	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2304186	PLAUR	cis	cerebellum	SCAN
rs2304186	ERCC1	cis	parietal	SCAN
rs2304186	ENSG00000105221	cis	multi-tissue	Pritchard
rs2304186	VASP	cis	cerebellum	SCAN
rs2304186	DMRTC2	cis	parietal	SCAN
rs2304186	TMEM91	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40732400-40740800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:40732600-40740400	Weak transcription	Brain Substantia Nigra	brain
3	chr19:40732800-40740800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:40732800-40740800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:40732800-40740800	Weak transcription	HMEC	breast
6	chr19:40732800-40759000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:40733000-40740800	Weak transcription	GM12878-XiMat	blood
8	chr19:40734000-40742000	Weak transcription	Small Intestine	intestine
9	chr19:40734800-40740200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:40735000-40740800	Weak transcription	Primary B cells from cord blood	blood
11	chr19:40735600-40757600	Weak transcription	Stomach Mucosa	stomach
12	chr19:40735800-40740400	Weak transcription	Aorta	Aorta
13	chr19:40735800-40748200	Weak transcription	Psoas Muscle	Psoas
14	chr19:40736000-40739800	Weak transcription	Primary T cells from cord blood	blood
15	chr19:40736000-40740000	Weak transcription	NHEK	skin
16	chr19:40736000-40740800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:40736200-40741000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr19:40736600-40741000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:40737200-40740600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:40737600-40748600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:40737600-40749600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:40737600-40751200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:40738000-40740000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:40738000-40740800	Weak transcription	HSMMtube	muscle
25	chr19:40738000-40742800	Weak transcription	Fetal Kidney	kidney
26	chr19:40738000-40744200	Strong transcription	Brain Anterior Caudate	brain
27	chr19:40738000-40746600	Strong transcription	Ovary	ovary
28	chr19:40738000-40747000	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:40738000-40748600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr19:40738000-40748800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:40738000-40749000	Strong transcription	Thymus	Thymus
32	chr19:40738000-40751600	Strong transcription	Dnd41	blood
33	chr19:40738000-40763800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:40738200-40740200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:40738200-40740600	Weak transcription	HUVEC	blood vessel
36	chr19:40738200-40740800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:40738200-40740800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:40738200-40740800	Weak transcription	Osteobl	bone
39	chr19:40738200-40741000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:40738200-40741200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr19:40738200-40742800	Weak transcription	NH-A	brain
42	chr19:40738200-40744000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr19:40738200-40745000	Weak transcription	HSMM	muscle
44	chr19:40738200-40748200	Strong transcription	Pancreas	Pancrea
45	chr19:40738200-40748600	Strong transcription	NHLF	lung
46	chr19:40738200-40748800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:40738200-40749000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:40738200-40756200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr19:40738400-40739800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr19:40738400-40740200	Weak transcription	Colon Smooth Muscle	Colon

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