Variant report

Variant	rs6542982
Chromosome Location	chr2:98269110-98269111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs17028771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17695937	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2071038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290126	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2922614	1.00[AMR][1000 genomes]
rs34459720	1.00[ASN][1000 genomes]
rs35321033	1.00[ASN][1000 genomes]
rs35530168	1.00[ASN][1000 genomes]
rs4069515	1.00[AMR][1000 genomes]
rs55757705	1.00[ASN][1000 genomes]
rs55766309	1.00[ASN][1000 genomes]
rs55933640	1.00[ASN][1000 genomes]
rs56035334	1.00[ASN][1000 genomes]
rs56233535	1.00[ASN][1000 genomes]
rs56717024	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58184071	1.00[AMR][1000 genomes]
rs58321192	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58383658	0.86[ASN][1000 genomes]
rs58738348	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59021370	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59060391	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59168350	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59523945	1.00[AMR][1000 genomes]
rs60226695	0.83[EUR][1000 genomes]
rs60753457	1.00[AMR][1000 genomes]
rs62157581	1.00[ASN][1000 genomes]
rs6716208	1.00[AMR][1000 genomes]
rs6727416	1.00[CEU][hapmap]
rs6753752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72942846	1.00[AMR][1000 genomes]
rs72942852	1.00[AMR][1000 genomes]
rs72942859	1.00[AMR][1000 genomes]
rs72942873	1.00[AMR][1000 genomes]
rs72946446	1.00[AMR][1000 genomes]
rs72946451	1.00[AMR][1000 genomes]
rs72947032	1.00[AMR][1000 genomes]
rs72947033	1.00[AMR][1000 genomes]
rs72947062	1.00[AMR][1000 genomes]
rs72949064	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949085	1.00[AMR][1000 genomes]
rs72949092	1.00[AMR][1000 genomes]
rs72949095	1.00[AMR][1000 genomes]
rs72951131	0.94[ASN][1000 genomes]
rs7425883	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7563002	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs7608385	0.94[LWK][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	nsv431402	chr2:97669032-98281634	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv535831	chr2:97671335-98270990	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	esv2752937	chr2:97708611-98269110	Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	esv2756939	chr2:97708611-98274527	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv2763630	chr2:97731133-98279050	Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv431413	chr2:97753585-98274527	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers 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	33 gene(s)	inside rSNPs	diseases
9	nsv1011958	chr2:97886322-98269110	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv1001249	chr2:97972600-98274527	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1005846	chr2:97972600-98281634	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
12	nsv1010905	chr2:98013814-98269110	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv1003384	chr2:98013814-98270884	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1010167	chr2:98013814-98273619	Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
15	nsv999627	chr2:98013814-98274527	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv1009263	chr2:98013814-98281634	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
17	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6542982	LOC375249	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98263200-98269400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:98263400-98272000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:98264000-98270600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:98264400-98270000	Weak transcription	Stomach Mucosa	stomach
5	chr2:98264600-98277400	Weak transcription	Right Atrium	heart
6	chr2:98265000-98270200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:98265000-98270400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:98265000-98270800	Weak transcription	Gastric	stomach
9	chr2:98265200-98270400	Weak transcription	Fetal Brain Male	brain
10	chr2:98265200-98270600	Weak transcription	Aorta	Aorta
11	chr2:98265200-98272000	Weak transcription	Brain Angular Gyrus	brain
12	chr2:98265200-98272800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:98265200-98276800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:98265200-98277200	Weak transcription	HUVEC	blood vessel
15	chr2:98265400-98273600	Weak transcription	Hela-S3	cervix
16	chr2:98265600-98270400	Weak transcription	Ovary	ovary
17	chr2:98265600-98274400	Weak transcription	Psoas Muscle	Psoas
18	chr2:98265600-98277600	Weak transcription	Small Intestine	intestine
19	chr2:98265600-98277800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:98265800-98269600	Weak transcription	Fetal Brain Female	brain
21	chr2:98265800-98270200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:98265800-98270400	Weak transcription	Fetal Kidney	kidney
23	chr2:98265800-98277200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:98266000-98270200	Weak transcription	NHLF	lung
25	chr2:98266000-98270400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:98266000-98272600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:98266000-98272800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:98266000-98272800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:98266000-98273000	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:98266200-98270000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:98266200-98270600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:98266200-98270600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:98266200-98270600	Weak transcription	Esophagus	oesophagus
34	chr2:98266200-98270800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:98266200-98270800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:98266200-98272600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:98266200-98272800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:98266400-98270200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:98266400-98270200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:98266400-98270200	Weak transcription	HSMM	muscle
41	chr2:98266400-98270200	Weak transcription	NHDF-Ad	bronchial
42	chr2:98266400-98270400	Weak transcription	Fetal Lung	lung
43	chr2:98266400-98270600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:98266400-98270600	Weak transcription	Dnd41	blood
45	chr2:98266400-98270800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:98266400-98271200	Weak transcription	Colonic Mucosa	Colon
47	chr2:98266400-98272600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:98266400-98272600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:98266400-98273000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:98266600-98269400	Weak transcription	Primary hematopoietic stem cells	blood

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