Variant report

Variant	rs2679409
Chromosome Location	chr2:128270109-128270110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128268468..128273715-chr2:128281746..128285691,7	MCF-7	breast:
2	chr2:128264079..128266201-chr2:128268340..128270505,2	MCF-7	breast:
3	chr2:128268636..128271128-chr2:128277665..128280504,3	K562	blood:
4	chr2:128256376..128258910-chr2:128269448..128271942,2	K562	blood:
5	chr2:128268475..128271778-chr2:128281782..128285622,5	K562	blood:
6	chr2:128268614..128270650-chr2:128272810..128274940,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163166	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10177052	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1019842	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496661	1.00[ASN][1000 genomes]
rs10803587	1.00[CHB][hapmap]
rs10803589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10850	1.00[ASN][1000 genomes]
rs11673952	0.81[CEU][hapmap]
rs11679414	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11680877	1.00[ASN][1000 genomes]
rs11683986	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11691916	1.00[ASN][1000 genomes]
rs11692990	1.00[ASN][1000 genomes]
rs12621149	0.81[CEU][hapmap]
rs13030463	1.00[ASN][1000 genomes]
rs1518760	1.00[ASN][1000 genomes]
rs1549767	0.82[CEU][hapmap]
rs1568278	1.00[ASN][1000 genomes]
rs17261845	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17261859	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1820969	1.00[ASN][1000 genomes]
rs1864552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864554	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052954	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069895	1.00[ASN][1000 genomes]
rs2069898	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2069902	1.00[ASN][1000 genomes]
rs2069904	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2069919	1.00[ASN][1000 genomes]
rs2099210	0.91[EUR][1000 genomes]
rs2163345	1.00[ASN][1000 genomes]
rs2163348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896979	1.00[ASN][1000 genomes]
rs334137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334138	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334154	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs334156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334157	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334158	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893897	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3958415	1.00[ASN][1000 genomes]
rs4662720	1.00[ASN][1000 genomes]
rs4662736	1.00[ASN][1000 genomes]
rs4662741	0.81[CEU][hapmap]
rs55998444	1.00[ASN][1000 genomes]
rs56273408	1.00[ASN][1000 genomes]
rs5937	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs59378658	1.00[ASN][1000 genomes]
rs61422716	1.00[ASN][1000 genomes]
rs6430938	1.00[ASN][1000 genomes]
rs6706077	0.81[CEU][hapmap]
rs6709113	0.86[CEU][hapmap]
rs6722447	0.82[CEU][hapmap]
rs6756535	1.00[ASN][1000 genomes]
rs72845975	1.00[ASN][1000 genomes]
rs72845976	1.00[ASN][1000 genomes]
rs72845991	1.00[ASN][1000 genomes]
rs72845993	1.00[ASN][1000 genomes]
rs72845997	1.00[ASN][1000 genomes]
rs72846002	1.00[ASN][1000 genomes]
rs72848604	1.00[ASN][1000 genomes]
rs72848612	1.00[ASN][1000 genomes]
rs72848615	1.00[ASN][1000 genomes]
rs72848616	1.00[ASN][1000 genomes]
rs72848618	1.00[ASN][1000 genomes]
rs7562428	1.00[ASN][1000 genomes]
rs7582598	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592490	0.88[EUR][1000 genomes]
rs7600934	0.81[CEU][hapmap]
rs7607907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs777554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs777569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891514	0.81[CEU][hapmap]
rs9287540	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128246200-128271800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:128262600-128283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:128263000-128272000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:128263000-128281200	Weak transcription	Fetal Kidney	kidney
5	chr2:128263200-128271400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:128263200-128271400	Weak transcription	Colonic Mucosa	Colon
7	chr2:128263200-128271600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:128263200-128271600	Weak transcription	Pancreas	Pancrea
9	chr2:128263200-128271600	Weak transcription	Spleen	Spleen
10	chr2:128263200-128271800	Weak transcription	Aorta	Aorta
11	chr2:128263200-128271800	Weak transcription	Brain Germinal Matrix	brain
12	chr2:128263200-128271800	Weak transcription	Esophagus	oesophagus
13	chr2:128263200-128282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:128263400-128271600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:128263400-128271600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:128263400-128271800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:128263400-128271800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:128263400-128275400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:128264600-128270200	Enhancers	Fetal Intestine Small	intestine
20	chr2:128265600-128272000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:128266000-128282800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:128266200-128271600	Weak transcription	Right Atrium	heart
23	chr2:128266600-128271000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:128266600-128271400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:128266600-128271400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:128266600-128271600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:128266600-128271600	Weak transcription	Fetal Brain Female	brain
28	chr2:128266600-128271600	Weak transcription	Lung	lung
29	chr2:128266600-128271600	Weak transcription	Ovary	ovary
30	chr2:128266600-128271800	Weak transcription	Fetal Lung	lung
31	chr2:128266600-128272000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:128266800-128270400	Enhancers	A549	lung
33	chr2:128266800-128271200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:128266800-128271400	Weak transcription	Fetal Stomach	stomach
35	chr2:128266800-128271400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:128266800-128271400	Weak transcription	HSMMtube	muscle
37	chr2:128266800-128271600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:128266800-128271800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:128266800-128272400	Weak transcription	HMEC	breast
40	chr2:128267000-128271600	Weak transcription	Brain Angular Gyrus	brain
41	chr2:128267000-128271600	Weak transcription	Brain Anterior Caudate	brain
42	chr2:128267200-128270200	Weak transcription	Left Ventricle	heart
43	chr2:128267200-128271400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:128267200-128271400	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:128267200-128271600	Weak transcription	Gastric	stomach
46	chr2:128267200-128274400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr2:128267200-128282000	Weak transcription	Fetal Brain Male	brain
48	chr2:128267400-128271600	Enhancers	Brain Substantia Nigra	brain
49	chr2:128267400-128273200	Strong transcription	Primary B cells from cord blood	blood
50	chr2:128267600-128272600	Strong transcription	Primary B cells from peripheral blood	blood

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