Variant report

Variant	rs6509938
Chromosome Location	chr19:55763409-55763410
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr19:55762917-55763482	GM12878	blood:	n/a	n/a
2	PBX3	chr19:55762914-55763501	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr19:55762786-55763513	HL-60	blood:	n/a	n/a
4	GATA2	chr19:55763054-55763419	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr19:55761204-55763469	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:55762898-55763478	K562	blood:	n/a	n/a
7	WRNIP1	chr19:55763395-55763559	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:55763331-55763409	K562	blood:	n/a	n/a
9	POLR2A	chr19:55762682-55763446	GM12892	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55725913..55730047-chr19:55761306..55765078,5	K562	blood:
2	chr19:55751418..55755269-chr19:55760609..55764390,3	K562	blood:
3	chr19:55762731..55764794-chr19:55917700..55919966,2	K562	blood:
4	chr19:55761266..55763802-chr19:55909842..55911559,2	K562	blood:
5	chr19:55748790..55751237-chr19:55759889..55763419,3	K562	blood:
6	chr19:55740826..55743029-chr19:55762405..55764201,3	K562	blood:
7	chr19:55758184..55761510-chr19:55762351..55764553,4	MCF-7	breast:
8	chr19:55731260..55733496-chr19:55763149..55766081,2	K562	blood:
9	chr19:55761815..55764585-chr19:55783782..55786476,2	K562	blood:
10	chr19:55761360..55765819-chr19:55917295..55921278,6	K562	blood:
11	chr19:55749737..55751772-chr19:55761919..55763681,2	K562	blood:

No data

Variant related genes	Relation type
PPP6R1	TF binding region
ENSG00000105063	Chromatin interaction
ENSG00000180089	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000267649	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10411896	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11665832	1.00[EUR][1000 genomes]
rs11667472	1.00[EUR][1000 genomes]
rs11669313	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11672373	1.00[CEU][hapmap];0.88[GIH][hapmap]
rs11672710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];1.00[EUR][1000 genomes]
rs11672774	1.00[EUR][1000 genomes]
rs35159664	0.96[EUR][1000 genomes]
rs3848608	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3848610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4337407	0.81[CHD][hapmap];0.88[GIH][hapmap]
rs4644955	0.96[GIH][hapmap]
rs4806651	0.97[ASN][1000 genomes]
rs4806652	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4806653	0.94[ASN][1000 genomes]
rs62126346	0.94[EUR][1000 genomes]
rs62126347	1.00[EUR][1000 genomes]
rs62126348	1.00[EUR][1000 genomes]
rs62126352	1.00[EUR][1000 genomes]
rs62126357	0.96[EUR][1000 genomes]
rs7258327	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8104509	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8105032	1.00[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912454	chr19:55725410-55783552	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
6	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
7	nsv912458	chr19:55763409-55823822	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55729400-55766200	Weak transcription	Fetal Brain Male	brain
2	chr19:55736800-55764200	Strong transcription	Dnd41	blood
3	chr19:55740400-55766000	Strong transcription	Fetal Stomach	stomach
4	chr19:55749200-55764400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:55750800-55767000	Weak transcription	HSMM	muscle
6	chr19:55754400-55765200	Weak transcription	Psoas Muscle	Psoas
7	chr19:55756000-55766400	Weak transcription	Small Intestine	intestine
8	chr19:55756400-55766600	Weak transcription	Fetal Kidney	kidney
9	chr19:55757000-55766200	Weak transcription	NHDF-Ad	bronchial
10	chr19:55757400-55767400	Weak transcription	Fetal Lung	lung
11	chr19:55757600-55767200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:55757600-55767600	Weak transcription	HSMMtube	muscle
13	chr19:55757600-55768200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:55758000-55768200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:55758200-55763600	Genic enhancers	Spleen	Spleen
16	chr19:55758200-55765200	Genic enhancers	Gastric	stomach
17	chr19:55758400-55763800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:55758400-55764000	Weak transcription	Brain Substantia Nigra	brain
19	chr19:55758400-55765200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:55758400-55765400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:55758400-55766200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:55758400-55767400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr19:55758400-55767600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:55758400-55769000	Weak transcription	Aorta	Aorta
25	chr19:55758600-55764600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr19:55758600-55765200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:55758600-55765800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr19:55758800-55765000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:55758800-55766200	Weak transcription	NHLF	lung
30	chr19:55758800-55767600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:55759400-55767200	Enhancers	Stomach Mucosa	stomach
32	chr19:55759600-55768200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:55760000-55764400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:55760000-55766600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:55760200-55763600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:55760400-55764000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr19:55760400-55764400	Weak transcription	Colon Smooth Muscle	Colon
38	chr19:55760400-55765200	Weak transcription	Brain Angular Gyrus	brain
39	chr19:55760400-55765400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:55760400-55766800	Weak transcription	Fetal Heart	heart
41	chr19:55760400-55766800	Weak transcription	HMEC	breast
42	chr19:55760400-55768600	Weak transcription	Ovary	ovary
43	chr19:55760800-55763800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:55760800-55766000	Strong transcription	Fetal Intestine Small	intestine
45	chr19:55761000-55763800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr19:55761200-55764200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr19:55761400-55763600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:55761400-55763800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
49	chr19:55761600-55765600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:55761600-55766200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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