Variant report

Variant	rs2207401
Chromosome Location	chr6:24882981-24882982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10946732	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946735	0.87[CEU][hapmap]
rs12111413	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192978	1.00[ASN][1000 genomes]
rs13211772	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13215106	1.00[ASN][1000 genomes]
rs13220782	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17671350	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207400	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2747678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747679	1.00[ASN][1000 genomes]
rs35158242	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35250553	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35953835	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61595405	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456637	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918387	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918511	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555168	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24855200-24895000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
2	chr6:24859400-24886800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:24862800-24885600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:24862800-24887400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
5	chr6:24870400-24883800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr6:24871800-24886800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:24874800-24883200	Weak transcription	Brain Anterior Caudate	brain
8	chr6:24874800-24883600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:24875600-24886800	Weak transcription	Fetal Heart	heart
10	chr6:24875800-24887800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:24876000-24901800	Weak transcription	Spleen	Spleen
12	chr6:24877000-24883000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:24877000-24888000	Genic enhancers	Primary T cells from cord blood	blood
14	chr6:24877400-24883400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:24877400-24888000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:24878400-24884000	Weak transcription	Esophagus	oesophagus
17	chr6:24878400-24887800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr6:24878400-24899800	Weak transcription	Thymus	Thymus
19	chr6:24878800-24885400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:24879200-24888200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:24879400-24883200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:24879800-24884400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:24880000-24889200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:24880200-24883600	Weak transcription	Osteobl	bone
25	chr6:24880200-24883800	Enhancers	Hela-S3	cervix
26	chr6:24880200-24886600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:24880400-24883600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:24880400-24888000	Weak transcription	Brain Germinal Matrix	brain
29	chr6:24880600-24883000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:24880600-24883400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:24880600-24886400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:24880600-24886600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:24880600-24886800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr6:24880600-24887200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:24880800-24883400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:24881000-24883200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr6:24881000-24886400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:24881200-24898400	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr6:24881400-24895400	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr6:24881600-24883400	Enhancers	GM12878-XiMat	blood
41	chr6:24881600-24888400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:24881800-24883600	Strong transcription	Fetal Thymus	thymus
43	chr6:24881800-24884000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr6:24881800-24891000	Weak transcription	Psoas Muscle	Psoas
45	chr6:24882000-24883800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:24882000-24884200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:24882000-24884400	Enhancers	NHDF-Ad	bronchial
48	chr6:24882000-24885600	Genic enhancers	Primary B cells from cord blood	blood
49	chr6:24882000-24887000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:24882200-24883200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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