Variant report

Variant	rs2238653
Chromosome Location	chr19:18950645-18950646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18882666..18885007-chr19:18949249..18951602,2	K562	blood:
2	chr19:18948748..18952215-chr19:18952430..18955166,3	MCF-7	breast:
3	chr19:18948977..18952233-chr19:18955408..18962693,8	MCF-7	breast:
4	chr19:18893741..18897746-chr19:18945981..18952333,7	K562	blood:
5	chr19:18950306..18952672-chr19:19042959..19045177,2	K562	blood:
6	chr19:18640795..18642364-chr19:18950530..18953348,2	K562	blood:

Variant related genes	Relation type
ENSG00000051128	Chromatin interaction
ENSG00000005007	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2238654	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238655	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238656	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238657	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808861	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808863	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4808871	0.80[ASN][1000 genomes]
rs59045002	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7408483	0.80[ASN][1000 genomes]
rs757115	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][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	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers 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	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv911299	chr19:18939954-18984843	Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 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	chr19:18945200-18951600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr19:18945200-18952200	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr19:18945200-18956600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:18945400-18952600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr19:18945600-18953200	Weak transcription	Aorta	Aorta
6	chr19:18945800-18952400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:18945800-18953000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:18945800-18955000	Genic enhancers	Fetal Intestine Small	intestine
9	chr19:18946000-18952600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:18946200-18958200	Weak transcription	Fetal Kidney	kidney
11	chr19:18946800-18950800	Weak transcription	Fetal Brain Male	brain
12	chr19:18947000-18952200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr19:18947200-18951200	Strong transcription	NHEK	skin
14	chr19:18947200-18958400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:18948200-18951400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:18948200-18951400	Enhancers	NHDF-Ad	bronchial
17	chr19:18948200-18951600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr19:18948200-18953200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:18948600-18951200	Strong transcription	Fetal Brain Female	brain
20	chr19:18948600-18957200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr19:18948800-18950800	Enhancers	HUVEC	blood vessel
22	chr19:18948800-18951800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr19:18948800-18954000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:18948800-18955800	Enhancers	Right Ventricle	heart
25	chr19:18948800-18956400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:18948800-18957800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:18948800-18958400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:18948800-18959000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr19:18949000-18951200	Enhancers	NHLF	lung
30	chr19:18949000-18951200	Enhancers	Osteobl	bone
31	chr19:18949000-18952200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:18949000-18954000	Weak transcription	Hela-S3	cervix
33	chr19:18949000-18954400	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr19:18949000-18955200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr19:18949200-18951000	Enhancers	Pancreas	Pancrea
36	chr19:18949200-18952000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr19:18949200-18955400	Enhancers	Liver	Liver
38	chr19:18949200-18956600	Enhancers	Left Ventricle	heart
39	chr19:18949200-18956800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr19:18949200-18958400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr19:18949400-18951000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:18949400-18951000	Enhancers	NH-A	brain
43	chr19:18949400-18951400	Enhancers	HSMM	muscle
44	chr19:18949600-18951000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr19:18949600-18951400	Enhancers	Small Intestine	intestine
46	chr19:18949600-18952200	Enhancers	Stomach Mucosa	stomach
47	chr19:18949800-18951000	Weak transcription	Primary T cells from cord blood	blood
48	chr19:18949800-18951200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:18949800-18952200	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr19:18949800-18953200	Enhancers	Brain Substantia Nigra	brain

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