Variant report

Variant	rs2972598
Chromosome Location	chr19:37839352-37839353
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11083424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1234256	0.89[YRI][hapmap]
rs1234261	0.89[YRI][hapmap]
rs16972024	0.81[CHD][hapmap]
rs16972028	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs17304779	1.00[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2112921	0.93[EUR][1000 genomes]
rs2305115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2921560	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2921563	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972597	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972600	0.88[ASN][1000 genomes]
rs320890	0.89[YRI][hapmap]
rs3745763	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs56743641	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56917663	0.93[EUR][1000 genomes]
rs59957425	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60159855	0.81[EUR][1000 genomes]
rs61290534	0.93[EUR][1000 genomes]
rs6508718	1.00[CEU][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes]
rs7247654	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7254780	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7255938	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[EUR][1000 genomes]
rs7259321	0.90[EUR][1000 genomes]
rs8100308	0.90[EUR][1000 genomes]
rs8109806	1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs8110164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv9718	chr19:37839070-37852872	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37826200-37853200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37826600-37848800	Weak transcription	Small Intestine	intestine
3	chr19:37826600-37856200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:37826600-37861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:37826800-37846600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:37826800-37847000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:37826800-37852600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:37826800-37853400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:37827000-37845800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:37827000-37853400	Weak transcription	Stomach Mucosa	stomach
11	chr19:37828000-37855800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:37830000-37846800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:37830000-37853600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:37830800-37853200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:37831800-37840400	Strong transcription	Ovary	ovary
16	chr19:37831800-37840600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:37831800-37842000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:37831800-37846400	Strong transcription	Dnd41	blood
19	chr19:37832000-37842000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr19:37832200-37840600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:37832200-37840800	Strong transcription	Primary T cells from cord blood	blood
22	chr19:37832200-37842000	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr19:37832600-37843200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:37832600-37852200	Weak transcription	Fetal Thymus	thymus
25	chr19:37832800-37850800	Weak transcription	HMEC	breast
26	chr19:37832800-37852400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:37833000-37845400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr19:37833600-37840800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:37833800-37840800	Strong transcription	Thymus	Thymus
30	chr19:37833800-37843400	Strong transcription	Adipose Nuclei	Adipose
31	chr19:37834200-37840200	ZNF genes & repeats	Liver	Liver
32	chr19:37834200-37841800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr19:37834400-37840000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:37834400-37840400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:37834400-37840400	Strong transcription	Fetal Lung	lung
36	chr19:37834400-37840800	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:37834400-37841600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:37834400-37842000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:37834400-37843000	Strong transcription	Placenta	Placenta
40	chr19:37834400-37843200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:37834400-37844200	Strong transcription	Fetal Stomach	stomach
42	chr19:37834400-37845200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:37834400-37847800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr19:37834600-37840000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:37834600-37840200	Strong transcription	Fetal Brain Female	brain
46	chr19:37834600-37840200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr19:37834600-37840400	Strong transcription	HSMMtube	muscle
48	chr19:37834600-37840600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:37834600-37840800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:37834600-37841400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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