Variant report

Variant	rs4544421
Chromosome Location	chr2:64097868-64097869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64097542..64099812-chr2:64100980..64103347,2	MCF-7	breast:
2	chr2:64095211..64099085-chr2:64100038..64104293,5	K562	blood:
3	chr2:64068214..64070648-chr2:64096231..64099054,2	MCF-7	breast:
4	chr2:64090294..64093479-chr2:64095197..64098946,3	K562	blood:
5	chr2:64068044..64070296-chr2:64097809..64100600,2	K562	blood:
6	chr2:63839924..63841875-chr2:64097480..64100299,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10166971	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10175674	0.89[CHB][hapmap]
rs12463827	0.82[EUR][1000 genomes]
rs12466966	0.93[EUR][1000 genomes]
rs12468093	0.84[EUR][1000 genomes]
rs12474366	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475294	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12988017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990604	0.94[EUR][1000 genomes]
rs12993544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12997303	0.85[EUR][1000 genomes]
rs12999675	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13005218	0.85[EUR][1000 genomes]
rs13007342	0.85[EUR][1000 genomes]
rs13007731	0.85[EUR][1000 genomes]
rs13009774	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs13010817	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014781	0.90[EUR][1000 genomes]
rs13023542	0.89[EUR][1000 genomes]
rs13025640	0.90[EUR][1000 genomes]
rs13028805	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034260	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345479	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1437455	0.86[EUR][1000 genomes]
rs1545196	0.85[EUR][1000 genomes]
rs171901	1.00[YRI][hapmap]
rs17555655	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17562312	0.91[EUR][1000 genomes]
rs17620012	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17701685	0.87[EUR][1000 genomes]
rs17701709	0.87[EUR][1000 genomes]
rs17752683	0.86[EUR][1000 genomes]
rs2287361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2422110	0.82[EUR][1000 genomes]
rs262536	1.00[YRI][hapmap]
rs34043307	0.88[EUR][1000 genomes]
rs34145077	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34196086	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34200806	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34239752	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34512058	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34900788	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35058898	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35122209	0.85[EUR][1000 genomes]
rs35247801	0.85[EUR][1000 genomes]
rs35253921	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35521527	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35552326	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35648996	0.89[EUR][1000 genomes]
rs35810427	0.91[EUR][1000 genomes]
rs35972278	0.92[EUR][1000 genomes]
rs35975566	0.94[EUR][1000 genomes]
rs36099158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815616	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3934536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075010	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4482470	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4599090	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]
rs4671072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671534	1.00[ASN][1000 genomes]
rs4671535	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4671537	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671538	0.86[EUR][1000 genomes]
rs66476638	0.93[EUR][1000 genomes]
rs66535980	0.87[EUR][1000 genomes]
rs66595136	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66650505	0.93[EUR][1000 genomes]
rs66660401	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66993685	0.86[EUR][1000 genomes]
rs6730664	0.82[EUR][1000 genomes]
rs67366434	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67962955	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71422402	0.82[EUR][1000 genomes]
rs72808216	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72808218	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72808231	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808248	0.94[EUR][1000 genomes]
rs72808254	0.93[EUR][1000 genomes]
rs72808262	0.94[EUR][1000 genomes]
rs72808287	0.85[EUR][1000 genomes]
rs874695	0.85[EUR][1000 genomes]
rs893779	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 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	chr2:64070200-64103000	Weak transcription	Gastric	stomach
2	chr2:64077000-64100200	Weak transcription	Ovary	ovary
3	chr2:64078000-64108000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:64081800-64100600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:64082200-64100200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:64082200-64110000	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:64083000-64123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:64083000-64129200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:64083200-64110200	Weak transcription	Small Intestine	intestine
10	chr2:64083200-64110600	Weak transcription	Pancreas	Pancrea
11	chr2:64084600-64100000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:64085400-64098000	Weak transcription	Lung	lung
13	chr2:64085400-64098000	Weak transcription	Psoas Muscle	Psoas
14	chr2:64085400-64098400	Weak transcription	Aorta	Aorta
15	chr2:64085400-64100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:64085400-64100600	Weak transcription	Spleen	Spleen
17	chr2:64085600-64102400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:64086600-64110000	Weak transcription	Esophagus	oesophagus
19	chr2:64086800-64100400	Weak transcription	Fetal Brain Female	brain
20	chr2:64086800-64100800	Weak transcription	Fetal Kidney	kidney
21	chr2:64086800-64102800	Weak transcription	Right Ventricle	heart
22	chr2:64087200-64099800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:64087600-64101800	Genic enhancers	Liver	Liver
24	chr2:64088000-64100000	Weak transcription	K562	blood
25	chr2:64088000-64107800	Weak transcription	Colonic Mucosa	Colon
26	chr2:64088800-64100600	Weak transcription	Fetal Stomach	stomach
27	chr2:64089000-64099800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:64089800-64101400	Weak transcription	Fetal Brain Male	brain
29	chr2:64090000-64102000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:64090200-64098600	Weak transcription	Hela-S3	cervix
31	chr2:64090200-64100600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:64090600-64100600	Weak transcription	Fetal Intestine Small	intestine
33	chr2:64090600-64102800	Weak transcription	Stomach Mucosa	stomach
34	chr2:64091400-64110000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:64091800-64098000	Weak transcription	NHLF	lung
36	chr2:64091800-64099200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:64091800-64107800	Weak transcription	Brain Germinal Matrix	brain
38	chr2:64092000-64099800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:64092000-64100000	Weak transcription	Fetal Lung	lung
40	chr2:64092000-64100000	Weak transcription	HSMMtube	muscle
41	chr2:64092000-64100000	Weak transcription	HUVEC	blood vessel
42	chr2:64092200-64099000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr2:64092600-64098000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:64092600-64099600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:64093000-64098600	Weak transcription	Placenta	Placenta
46	chr2:64093000-64098800	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:64093000-64099800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:64093000-64100000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:64093000-64100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:64093000-64100200	Weak transcription	Fetal Intestine Large	intestine

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