Variant report

Variant	rs2604902
Chromosome Location	chr19:41115040-41115041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41114826-41117365	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:41114946-41117153	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr19:41114805-41117539	K562	blood:	n/a	n/a
4	POLR2A	chr19:41114965-41117433	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:41114825-41115047	HCT-116	colon:	n/a	n/a
6	POLR2A	chr19:41114932-41116294	K562	blood:	n/a	n/a
7	POLR2A	chr19:41114887-41117244	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40947602..40950295-chr19:41114097..41116019,2	MCF-7	breast:
2	chr19:41082563..41084216-chr19:41114074..41116543,2	K562	blood:
3	chr19:40929828..40933213-chr19:41114237..41116915,3	MCF-7	breast:
4	chr19:40949481..40951384-chr19:41114617..41116181,2	MCF-7	breast:
5	chr19:41114462..41116761-chr19:41130129..41133109,2	MCF-7	breast:
6	chr19:41104685..41106959-chr19:41114610..41116415,2	MCF-7	breast:
7	chr19:41113914..41116044-chr19:41221538..41224427,3	MCF-7	breast:

No data

Variant related genes	Relation type
LTBP4	TF binding region
RN7SL758P	TF binding region
ENSG00000197019	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000086544	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10402698	0.80[ASN][1000 genomes]
rs10403467	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10403833	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10403963	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10405930	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10410606	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1051303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083561	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1131620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11667706	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11667772	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668582	0.92[EUR][1000 genomes]
rs12610819	0.83[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap]
rs12611045	0.96[ASN][1000 genomes]
rs12980111	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1318544	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1864074	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864078	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869712	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278242	0.83[CHB][hapmap]
rs2278246	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303727	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303729	0.86[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2369006	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs28571670	0.85[AMR][1000 genomes]
rs28649715	0.96[ASN][1000 genomes]
rs28655571	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs392726	0.94[CHB][hapmap];0.93[CHD][hapmap];0.84[LWK][hapmap];0.88[ASN][1000 genomes]
rs393569	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs396118	0.87[ASN][1000 genomes]
rs404584	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs406133	0.83[ASN][1000 genomes]
rs410101	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs413901	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs415075	0.84[ASN][1000 genomes]
rs420720	0.86[ASN][1000 genomes]
rs4803348	0.96[ASN][1000 genomes]
rs56353506	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7171	0.88[ASN][1000 genomes]
rs7257696	0.81[CHD][hapmap]
rs7259067	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259237	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259554	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919307	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2604902	QPCTL	cis	cerebellum	SCAN
rs2604902	CA11	cis	cerebellum	SCAN
rs2604902	ZNF296	cis	cerebellum	SCAN
rs2604902	PGLYRP1	cis	cerebellum	SCAN
rs2604902	B9D2	cis	parietal	SCAN
rs2604902	CEACAM6	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41106000-41136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41109800-41122600	Weak transcription	Aorta	Aorta
3	chr19:41110000-41118200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:41112000-41115200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:41112000-41115200	Weak transcription	HUVEC	blood vessel
6	chr19:41112000-41115600	Weak transcription	Brain Angular Gyrus	brain
7	chr19:41112000-41115600	Weak transcription	Brain Anterior Caudate	brain
8	chr19:41112000-41116000	Enhancers	Stomach Mucosa	stomach
9	chr19:41112000-41116200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:41112000-41116200	Weak transcription	NHLF	lung
11	chr19:41112200-41115200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:41112200-41115200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:41112200-41115200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:41112200-41115200	Weak transcription	Fetal Lung	lung
15	chr19:41112200-41115200	Weak transcription	Osteobl	bone
16	chr19:41112200-41115400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr19:41112200-41115400	Weak transcription	Gastric	stomach
18	chr19:41112200-41115400	Weak transcription	Psoas Muscle	Psoas
19	chr19:41112200-41115400	Weak transcription	Small Intestine	intestine
20	chr19:41112200-41115400	Weak transcription	HSMM	muscle
21	chr19:41112400-41115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:41112400-41115200	Enhancers	Primary T cells fromperipheralblood	blood
23	chr19:41112400-41115200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:41112400-41115200	Enhancers	Fetal Intestine Large	intestine
25	chr19:41112600-41115200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:41112600-41115200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:41112600-41115200	Weak transcription	HMEC	breast
28	chr19:41113000-41115400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr19:41113200-41115400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:41113200-41115400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:41113200-41115400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr19:41113600-41115200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:41113600-41115200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:41113800-41115200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr19:41113800-41115200	Enhancers	Duodenum Mucosa	Duodenum
36	chr19:41113800-41115400	Weak transcription	Left Ventricle	heart
37	chr19:41114000-41115200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:41114000-41115200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:41114000-41115200	Weak transcription	Pancreas	Pancrea
40	chr19:41114200-41115200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:41114200-41115200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr19:41114200-41115200	Weak transcription	Right Ventricle	heart
43	chr19:41114200-41115400	Weak transcription	Lung	lung
44	chr19:41114200-41115400	Weak transcription	Right Atrium	heart
45	chr19:41114400-41115200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr19:41114400-41115200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:41114400-41115200	Weak transcription	Colonic Mucosa	Colon
48	chr19:41114400-41115200	Weak transcription	A549	lung
49	chr19:41114400-41115400	Weak transcription	Esophagus	oesophagus
50	chr19:41114400-41115400	Weak transcription	Spleen	Spleen

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