Variant report

Variant	rs7246479
Chromosome Location	chr19:55824332-55824333
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:55824155-55824579	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:55824330-55824465	K562	blood:	n/a	n/a
3	POLR2A	chr19:55824030-55825180	K562	blood:	n/a	n/a
4	POLR2A	chr19:55824032-55825550	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:55824196-55824392	HCT-116	colon:	n/a	n/a
6	POLR2A	chr19:55824318-55824531	MCF-7	breast:	n/a	n/a
7	POLR2A	chr19:55823924-55824636	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:55824301-55824438	A549	lung:	n/a	n/a
9	POLR2A	chr19:55823921-55824869	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:55824171-55825239	H1-neurons	neurons:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:55824316-55824366	HIPEpiC	eye:	n/a
2	chr19:55824316-55824366	HEEpiC	esophagus:	n/a
3	chr19:55824316-55824366	HRPEpiC	eye:	n/a
4	chr19:55824316-55824366	Hepatocyte	liver:	n/a
5	chr19:55824316-55824366	HRE	kidney:	n/a
6	chr19:55824316-55824366	GM12891	blood:	n/a
7	chr19:55824316-55824366	HEK293	kidney:	embryo
8	chr19:55824316-55824366	HAEpiC	amniotic membrane:	n/a
9	chr19:55824316-55824366	HNPCEpiC	eye:	n/a
10	chr19:55824316-55824366	HRCEpiC	kidney:	n/a
11	chr19:55824316-55824366	GM06990	blood:	n/a
12	chr19:55824316-55824366	BJ	skin:	n/a
13	chr19:55824316-55824366	SK-N-SH_RA	brain:	n/a
14	chr19:55824316-55824366	PrEC	prostate:	n/a
15	chr19:55824316-55824366	HCPEpiC	choroid plexus:	n/a
16	chr19:55824316-55824366	SKMC	muscle:	n/a
17	chr19:55824316-55824366	RPTEC	kidney:	n/a
18	chr19:55824316-55824366	HepG2	liver:	n/a
19	chr19:55824316-55824366	AoSMC	blood vessel:	n/a
20	chr19:55824316-55824366	NB4	blood:	n/a
21	chr19:55824316-55824366	HL-60	blood:	n/a
22	chr19:55824316-55824366	ECC-1	luminal epithelium:	n/a
23	chr19:55824316-55824366	U87	brain:	n/a
24	chr19:55824316-55824366	H1-hESC	embryonic stem cell:	embryo
25	chr19:55824316-55824366	CMK	blood:	n/a
26	chr19:55824316-55824366	AG09319	gingival:	n/a
27	chr19:55824316-55824366	MCF10A-Er-Src	breast:	n/a
28	chr19:55824316-55824366	HCM	heart:	n/a
29	chr19:55824316-55824366	NHBE	bronchial:	n/a
30	chr19:55824316-55824366	GM12892	blood:	n/a
31	chr19:55824316-55824366	LNCaP	prostate:	n/a
32	chr19:55824316-55824366	HMEC	breast:	n/a
33	chr19:55824316-55824366	ovcar-3	ovarian:	n/a
34	chr19:55824316-55824366	PANC-1	pancreas:	n/a
35	chr19:55824316-55824366	ProgFib	skin:	n/a
36	chr19:55824316-55824366	HCF	heart:	n/a
37	chr19:55824316-55824366	SK-N-SH	brain:	n/a
38	chr19:55824316-55824366	K562	blood:	n/a
39	chr19:55824316-55824366	GM19239	blood:	n/a
40	chr19:55824316-55824366	AG10803	skin:	n/a
41	chr19:55824316-55824366	AG09309	skin:	n/a
42	chr19:55824316-55824366	GM12878	blood:	n/a
43	chr19:55824316-55824366	SK-N-MC	brain:	n/a
44	chr19:55824316-55824366	MCF-7	breast:	n/a
45	chr19:55824316-55824366	HPAEpiC	pulmonary alveolar:	n/a
46	chr19:55824316-55824366	Jurkat	blood:	n/a
47	chr19:55824316-55824366	HUVEC	blood vessel:	n/a
48	chr19:55824316-55824366	A549	lung:	n/a
49	chr19:55824316-55824366	PFSK-1	brain:	n/a
50	chr19:55824316-55824366	T-47D	breast:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55823194..55826152-chr19:55862639..55864408,2	MCF-7	breast:
2	chr19:55823464..55826330-chr19:55895839..55897865,2	K562	blood:
3	chr19:55819947..55823832-chr19:55824271..55826603,6	K562	blood:
4	chr19:55822211..55824840-chr19:55897185..55900181,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268729	TF binding region
ENSG00000268729	CpG island
ENSG00000108107	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000160471	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10411773	0.92[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs10412726	0.92[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs1172820	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11882930	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2384688	0.94[EUR][1000 genomes]
rs2384689	0.94[EUR][1000 genomes]
rs2384691	0.94[EUR][1000 genomes]
rs4806659	0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7252864	0.86[AMR][1000 genomes]
rs734518	0.92[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs7508682	0.89[EUR][1000 genomes]
rs8113016	0.84[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes]
rs897797	0.92[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs897798	0.93[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	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
5	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
6	nsv912459	chr19:55791380-55845386	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
8	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7246479	RPS5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55797400-55824600	Weak transcription	Gastric	stomach
2	chr19:55813200-55825200	Weak transcription	Left Ventricle	heart
3	chr19:55813200-55827600	Weak transcription	Lung	lung
4	chr19:55813400-55825000	Strong transcription	Brain Germinal Matrix	brain
5	chr19:55813600-55824800	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:55813600-55827400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:55813600-55850000	Weak transcription	Right Atrium	heart
8	chr19:55813800-55824400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr19:55813800-55827600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:55814000-55824600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:55814000-55825200	Strong transcription	Fetal Brain Female	brain
12	chr19:55814000-55827600	Weak transcription	A549	lung
13	chr19:55814200-55825000	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr19:55814400-55824600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:55814400-55831400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr19:55817600-55824800	Weak transcription	K562	blood
17	chr19:55818200-55827400	Weak transcription	Aorta	Aorta
18	chr19:55818200-55832400	Weak transcription	Colonic Mucosa	Colon
19	chr19:55818400-55824600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:55818400-55831000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:55818600-55831200	Weak transcription	Right Ventricle	heart
22	chr19:55818800-55824600	Weak transcription	Thymus	Thymus
23	chr19:55820800-55839000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr19:55821000-55831000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:55821000-55831200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:55821200-55824800	Weak transcription	Fetal Kidney	kidney
27	chr19:55821400-55824600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:55821400-55825600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr19:55821400-55825800	Strong transcription	Fetal Intestine Small	intestine
30	chr19:55821400-55827200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:55821400-55827600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr19:55821400-55831000	Weak transcription	Osteobl	bone
33	chr19:55821600-55825200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:55821600-55827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:55821600-55827600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr19:55821800-55829400	Weak transcription	NHLF	lung
37	chr19:55821800-55831000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:55821800-55831000	Weak transcription	Fetal Brain Male	brain
39	chr19:55821800-55831200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:55822000-55824400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:55822000-55824400	Weak transcription	Brain Hippocampus Middle	brain
42	chr19:55822000-55824600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr19:55822000-55824800	Weak transcription	HepG2	liver
44	chr19:55822000-55825600	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:55822000-55825800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr19:55822000-55831000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:55822000-55831400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:55822200-55831000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr19:55822200-55831000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr19:55822200-55831000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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