Variant report

Variant	rs2368477
Chromosome Location	chr19:39112862-39112863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39112747-39112946	K562	blood:	n/a	n/a
2	POLR2A	chr19:39108158-39113791	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39112082..39114534-chr19:39125989..39129017,3	MCF-7	breast:

Variant related genes	Relation type
MAP4K1	TF binding region
EIF3K	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1004795	1.00[CEU][hapmap]
rs1004796	1.00[CEU][hapmap]
rs10404936	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10408694	1.00[CEU][hapmap]
rs10408718	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10413936	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12459780	1.00[CEU][hapmap]
rs12461431	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12461789	1.00[CEU][hapmap]
rs13344413	1.00[LWK][hapmap]
rs13345914	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17847678	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1966386	0.85[AFR][1000 genomes]
rs1978444	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2098657	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2287731	0.83[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2287734	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2287735	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2292800	1.00[CEU][hapmap]
rs2292801	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2303040	1.00[LWK][hapmap]
rs2303041	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3786830	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs3786839	1.00[LWK][hapmap]
rs3786844	1.00[TSI][hapmap]
rs4801804	0.85[AFR][1000 genomes]
rs4802582	1.00[CEU][hapmap]
rs4802583	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs4802584	1.00[CEU][hapmap]
rs4802589	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs4802618	1.00[CEU][hapmap]
rs55922338	0.80[AMR][1000 genomes]
rs59727665	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508809	1.00[CEU][hapmap]
rs73552634	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs750437	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking 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	37 gene(s)	inside rSNPs	diseases
4	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
7	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39110400-39122600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39110800-39113000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:39110800-39114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:39110800-39114400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:39110800-39118000	Weak transcription	Fetal Kidney	kidney
6	chr19:39110800-39120800	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr19:39110800-39120800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:39111000-39121000	Strong transcription	Ovary	ovary
9	chr19:39111000-39121600	Strong transcription	Fetal Intestine Large	intestine
10	chr19:39111000-39122600	Strong transcription	Fetal Intestine Small	intestine
11	chr19:39111000-39124000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr19:39111000-39124400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:39111000-39124600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:39111000-39125000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:39111000-39127000	Strong transcription	Thymus	Thymus
16	chr19:39111000-39127400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr19:39111000-39128800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:39111200-39113000	Strong transcription	Brain Substantia Nigra	brain
19	chr19:39111200-39113000	Strong transcription	GM12878-XiMat	blood
20	chr19:39111200-39113200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:39111200-39113200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:39111200-39113200	Strong transcription	Colon Smooth Muscle	Colon
23	chr19:39111200-39113200	Strong transcription	Spleen	Spleen
24	chr19:39111200-39113200	Strong transcription	K562	blood
25	chr19:39111200-39113400	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr19:39111200-39113400	Strong transcription	Brain Hippocampus Middle	brain
27	chr19:39111200-39113800	Strong transcription	A549	lung
28	chr19:39111200-39114400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr19:39111200-39114400	Weak transcription	Stomach Mucosa	stomach
30	chr19:39111200-39114400	Weak transcription	Hela-S3	cervix
31	chr19:39111200-39114400	Weak transcription	HepG2	liver
32	chr19:39111200-39114600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:39111200-39114600	Weak transcription	Psoas Muscle	Psoas
34	chr19:39111200-39115400	Strong transcription	Pancreas	Pancrea
35	chr19:39111200-39116400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:39111200-39118200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr19:39111200-39120600	Strong transcription	HMEC	breast
38	chr19:39111200-39120800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:39111200-39120800	Strong transcription	Gastric	stomach
40	chr19:39111200-39120800	Strong transcription	HUVEC	blood vessel
41	chr19:39111200-39121000	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr19:39111200-39121400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:39111200-39121400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:39111200-39121600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:39111200-39121600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:39111200-39121600	Strong transcription	Right Ventricle	heart
47	chr19:39111200-39121800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr19:39111200-39121800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:39111200-39122200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:39111200-39122400	Strong transcription	Colonic Mucosa	Colon

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