Variant report

Variant	rs602850
Chromosome Location	chr11:107681105-107681106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1680252	0.86[EUR][1000 genomes]
rs495836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500063	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs503951	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs516091	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs518073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs519965	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs534359	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs537312	0.82[EUR][1000 genomes]
rs542160	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs553663	0.84[JPT][hapmap]
rs556153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs562528	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs566804	0.88[ASN][1000 genomes]
rs567794	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs569545	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs570503	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs571418	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs573280	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs575993	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs629278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs670456	0.88[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1039425	chr11:107468681-107895836	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv427899	chr11:107471544-107805894	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1052198	chr11:107509918-107684371	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1049524	chr11:107540937-107954011	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1038581	chr11:107564274-107838386	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv898378	chr11:107580985-107847983	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv521771	chr11:107590335-107904646	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1048938	chr11:107604473-107929950	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
10	nsv556381	chr11:107644296-107684371	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv468867	chr11:107649026-107697633	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv556382	chr11:107649026-107697633	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv1035229	chr11:107653731-107717190	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs602850	SLC35F2	cis	Stomach	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107661000-107693200	Weak transcription	Spleen	Spleen
2	chr11:107661800-107685800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:107661800-107691800	Weak transcription	Esophagus	oesophagus
4	chr11:107662400-107682800	Weak transcription	Pancreas	Pancrea
5	chr11:107662400-107686400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:107662800-107683800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:107663000-107682800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:107663000-107683400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:107663000-107683600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:107663200-107684200	Weak transcription	HepG2	liver
11	chr11:107663200-107690200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:107663600-107682200	Weak transcription	Ovary	ovary
13	chr11:107664600-107683800	Weak transcription	Stomach Mucosa	stomach
14	chr11:107664600-107686000	Weak transcription	Gastric	stomach
15	chr11:107670800-107685000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:107671200-107682600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:107671200-107682600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:107671600-107685000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:107671600-107685800	Weak transcription	HSMM	muscle
20	chr11:107671600-107686200	Weak transcription	NHDF-Ad	bronchial
21	chr11:107672000-107697000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:107672800-107687800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:107673000-107682400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:107673000-107683200	Strong transcription	HUVEC	blood vessel
25	chr11:107673400-107727800	Weak transcription	Primary B cells from cord blood	blood
26	chr11:107673600-107682200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr11:107673600-107689800	Weak transcription	HMEC	breast
28	chr11:107674400-107691800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr11:107675800-107682600	Strong transcription	NHEK	skin
30	chr11:107676200-107684600	Strong transcription	GM12878-XiMat	blood
31	chr11:107676200-107684800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:107676400-107690000	Weak transcription	A549	lung
33	chr11:107676400-107694200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr11:107676600-107682200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:107676800-107684000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr11:107677800-107681800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:107677800-107683600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:107677800-107686200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:107677800-107689600	Weak transcription	NH-A	brain
40	chr11:107677800-107691800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:107678200-107684800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:107679000-107687600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:107679000-107691600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:107679000-107696400	Weak transcription	Lung	lung
45	chr11:107679200-107685000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:107679600-107685800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:107679600-107691800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr11:107680000-107682400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr11:107680000-107687400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr11:107680400-107681400	Enhancers	Fetal Intestine Small	intestine

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