Variant report

Variant	rs2842509
Chromosome Location	chr6:38036566-38036567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38035459..38038429-chr6:38039694..38042132,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11963886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496579	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890244	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890367	0.90[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2495213	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645103	1.00[ASN][1000 genomes]
rs2645119	1.00[MEX][hapmap]
rs2645129	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2645133	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645135	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645136	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2645138	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2749920	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2842501	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2842504	1.00[ASN][1000 genomes]
rs2842518	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs2842519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458033	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6930917	1.00[CEU][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765420	1.00[ASN][1000 genomes]
rs7775465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380711	1.00[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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38017200-38055000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:38020400-38046200	Weak transcription	Stomach Mucosa	stomach
3	chr6:38023000-38054800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:38023200-38052800	Weak transcription	Gastric	stomach
5	chr6:38024400-38040000	Weak transcription	Fetal Heart	heart
6	chr6:38024600-38041800	Weak transcription	Fetal Brain Male	brain
7	chr6:38024600-38045000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:38026000-38047600	Weak transcription	Hela-S3	cervix
9	chr6:38026200-38053800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:38028400-38036800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr6:38030400-38037800	Weak transcription	Pancreas	Pancrea
12	chr6:38030800-38036600	Weak transcription	Fetal Intestine Small	intestine
13	chr6:38030800-38041600	Weak transcription	HMEC	breast
14	chr6:38030800-38085800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:38031400-38039400	Weak transcription	K562	blood
16	chr6:38031400-38042400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:38031400-38045000	Weak transcription	Aorta	Aorta
18	chr6:38031400-38052400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:38031600-38037200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:38031600-38039800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:38031600-38048200	Weak transcription	HUVEC	blood vessel
22	chr6:38031600-38048600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:38031600-38049400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:38031600-38053200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:38031600-38059600	Weak transcription	Spleen	Spleen
26	chr6:38031600-38061600	Weak transcription	Brain Germinal Matrix	brain
27	chr6:38031800-38036600	Weak transcription	Fetal Lung	lung
28	chr6:38031800-38045400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:38032000-38052600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:38032000-38052600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:38032200-38037800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:38032200-38039600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:38032200-38039800	Weak transcription	Brain Angular Gyrus	brain
34	chr6:38032200-38042200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:38032200-38044800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:38032200-38048200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:38032200-38048400	Weak transcription	HSMM	muscle
38	chr6:38032200-38048600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:38032200-38051400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:38032400-38045200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr6:38032400-38045400	Weak transcription	A549	lung
42	chr6:38032400-38050800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:38032400-38056200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:38032800-38038800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:38032800-38046400	Weak transcription	Osteobl	bone
46	chr6:38032800-38046600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:38032800-38046800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr6:38032800-38050000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:38032800-38050000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr6:38032800-38050000	Weak transcription	Dnd41	blood

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