Variant report

Variant	rs10403081
Chromosome Location	chr19:42414422-42414423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:42414389-42415428	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:42414262-42415829	HL-60	blood:	n/a	n/a
3	POLR2A	chr19:42413937-42416175	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr19:42413266-42416121	K562	blood:	n/a	n/a
5	POLR2A	chr19:42413672-42416851	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:42413194-42414536	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr19:42414321-42416435	GM12891	blood:	n/a	n/a
8	ZNF263	chr19:42413735-42414529	HEK293-T-REx	kidney:	n/a	chr19:42413847-42413856 chr19:42414392-42414401
9	POLR2A	chr19:42413748-42416743	GM12891	blood:	n/a	n/a
10	POLR2A	chr19:42414422-42415403	GM12878	blood:	n/a	n/a
11	BCL3	chr19:42414149-42415542	A549	lung:	n/a	n/a
12	POLR2A	chr19:42414054-42415102	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:42412043-42416925	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:42412744-42416335	GM18505	blood:	n/a	n/a
15	POLR2A	chr19:42413807-42415543	PFSK-1	brain:	n/a	n/a
16	PML	chr19:42414377-42414736	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:42414399-42415435	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:42414048-42415605	GM12891	blood:	n/a	n/a
19	POLR2A	chr19:42412083-42416861	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:42414344-42414639	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr19:42414066-42416690	U87	brain:	n/a	n/a
22	JUN	chr19:42414343-42414492	K562	blood:	n/a	n/a
23	POLR2A	chr19:42414018-42414492	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:42414282-42414900	HUVEC	blood vessel:	n/a	n/a
25	BCL3	chr19:42414159-42415915	A549	lung:	n/a	n/a
26	POLR2A	chr19:42414065-42416690	U87	brain:	n/a	n/a
27	POLR2A	chr19:42414162-42414544	U87	brain:	n/a	n/a
28	POLR2A	chr19:42414166-42414578	U87	brain:	n/a	n/a
29	POLR2A	chr19:42413247-42416753	GM12892	blood:	n/a	n/a
30	POLR2A	chr19:42414263-42416523	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr19:42412767-42414572	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr19:42412700-42416805	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:42414223-42415747	HL-60	blood:	n/a	n/a
34	POLR2A	chr19:42414198-42414912	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr19:42412681-42416659	A549	lung:	n/a	n/a
36	POLR2A	chr19:42413690-42415621	HepG2	liver:	n/a	n/a
37	NFATC1	chr19:42414375-42414776	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:42412140-42416485	K562	blood:	n/a	n/a
39	POLR2A	chr19:42412121-42416922	GM12892	blood:	n/a	n/a
40	MTA3	chr19:42414327-42415694	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:42412075-42416779	SK-N-MC	brain:	n/a	n/a
42	POLR2A	chr19:42414416-42414437	Hela-S3	cervix:	n/a	n/a
43	TCF12	chr19:42414420-42416661	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42400938..42403112-chr19:42412847..42414847,2	MCF-7	breast:
2	chr19:42406489..42409925-chr19:42413611..42416710,4	K562	blood:
3	chr19:42407772..42411584-chr19:42411987..42415149,3	MCF-7	breast:
4	chr19:42386109..42390387-chr19:42411996..42416642,6	K562	blood:
5	chr19:42400409..42404033-chr19:42410840..42416491,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268041	TF binding region
ENSG00000076928	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10401189	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10401937	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10402667	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417495	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10419314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11878536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11878555	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12104228	1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16975619	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288509	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288510	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288511	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288512	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303798	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28396197	0.89[AMR][1000 genomes]
rs28521795	0.89[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28706300	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3745222	0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6509003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs717225	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7252790	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252800	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7253691	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7260129	0.83[AMR][1000 genomes]
rs73550603	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550610	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73550618	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8109784	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109959	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8110305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8113339	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8113686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs891169	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs891170	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs891171	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891172	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS 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	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
2	chr19:42396800-42415200	Strong transcription	Dnd41	blood
3	chr19:42410000-42414800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:42410600-42415400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:42410800-42415000	Weak transcription	NH-A	brain
6	chr19:42411200-42414800	Weak transcription	Fetal Lung	lung
7	chr19:42411200-42415000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:42411200-42415200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:42411200-42415800	Weak transcription	Primary B cells from cord blood	blood
10	chr19:42411400-42414600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr19:42411400-42414800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:42411400-42414800	Weak transcription	Small Intestine	intestine
13	chr19:42411400-42415000	Weak transcription	Esophagus	oesophagus
14	chr19:42411400-42415200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr19:42411400-42415600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:42411400-42415800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:42411400-42416200	Weak transcription	Pancreas	Pancrea
18	chr19:42411600-42414800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:42411600-42414800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:42411600-42415600	Weak transcription	Left Ventricle	heart
21	chr19:42411600-42415800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:42411600-42415800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr19:42411800-42414800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:42411800-42416000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:42411800-42416000	Weak transcription	Brain Substantia Nigra	brain
26	chr19:42411800-42416000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:42411800-42416000	Weak transcription	GM12878-XiMat	blood
28	chr19:42412400-42414600	Weak transcription	Right Ventricle	heart
29	chr19:42412400-42414800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr19:42412400-42415000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:42412600-42414800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:42412600-42415800	Weak transcription	Spleen	Spleen
33	chr19:42412600-42416600	Weak transcription	Gastric	stomach
34	chr19:42412600-42419600	Weak transcription	Ovary	ovary
35	chr19:42412800-42414600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:42412800-42414600	Weak transcription	Lung	lung
37	chr19:42413000-42414600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:42413200-42414600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:42413200-42414800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:42413200-42414800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:42413200-42415000	Weak transcription	Primary T cells from cord blood	blood
42	chr19:42413400-42415000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:42413400-42415200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:42413600-42414600	Weak transcription	Thymus	Thymus
45	chr19:42413600-42414800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:42413600-42414800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr19:42414000-42414800	Weak transcription	Fetal Intestine Small	intestine
48	chr19:42414200-42415000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
49	chr19:42414200-42416400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr19:42414400-42414600	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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