Variant report

Variant	rs13405400
Chromosome Location	chr2:100088332-100088333
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100084922..100089797-chr2:100104456..100108052,9	MCF-7	breast:
2	chr2:100086031..100088660-chr2:100104187..100107882,3	MCF-7	breast:
3	chr2:100066768..100070769-chr2:100085883..100089135,3	K562	blood:
4	chr2:100078933..100081024-chr2:100087446..100090857,3	K562	blood:
5	chr2:100087595..100089096-chr2:100090818..100093356,2	K562	blood:

Variant related genes	Relation type
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10173883	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175852	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176205	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179343	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179435	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179697	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180138	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180688	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182492	0.84[EUR][1000 genomes]
rs10186223	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191001	0.88[ASN][1000 genomes]
rs10207435	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210257	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210346	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496337	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123776	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123778	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123783	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12162367	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617324	0.83[EUR][1000 genomes]
rs12623835	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989521	0.82[EUR][1000 genomes]
rs12992356	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001438	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017843	0.86[EUR][1000 genomes]
rs13028722	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384665	0.94[ASN][1000 genomes]
rs13394927	0.84[EUR][1000 genomes]
rs13401163	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402784	0.83[EUR][1000 genomes]
rs13409359	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415713	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416265	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419448	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420087	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420293	0.84[EUR][1000 genomes]
rs13426758	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427424	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429185	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429806	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13430662	0.81[ASN][1000 genomes]
rs13430962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431410	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13432046	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376444	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17022653	0.84[EUR][1000 genomes]
rs17022663	0.84[EUR][1000 genomes]
rs1882598	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922625	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1922627	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1948101	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309577	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309615	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309616	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28369929	0.85[EUR][1000 genomes]
rs28369949	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382945	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382947	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382955	0.84[EUR][1000 genomes]
rs28745279	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087399	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792151	0.84[EUR][1000 genomes]
rs3828162	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522654	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4850902	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851197	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851199	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851201	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542877	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706425	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712137	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721031	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726711	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744199	0.81[EUR][1000 genomes]
rs6745645	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749029	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72815074	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72815086	0.81[EUR][1000 genomes]
rs72817011	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7567230	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7567462	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7569805	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579143	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579171	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581337	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582085	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582133	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584022	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584705	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7585532	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7599384	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599843	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603388	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606279	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9308819	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308821	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308823	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973846	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv874700	chr2:100062163-100099989	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
2	chr2:100048200-100090600	Weak transcription	Stomach Mucosa	stomach
3	chr2:100055800-100089000	Weak transcription	Pancreas	Pancrea
4	chr2:100055800-100092600	Weak transcription	Gastric	stomach
5	chr2:100056600-100091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:100073400-100090000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:100075200-100090400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:100075200-100103000	Weak transcription	Hela-S3	cervix
9	chr2:100076200-100098400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:100076200-100105000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:100076600-100094800	Weak transcription	Spleen	Spleen
12	chr2:100076600-100104200	Weak transcription	NHLF	lung
13	chr2:100078600-100088600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:100078600-100088800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:100078600-100091000	Weak transcription	Aorta	Aorta
16	chr2:100078600-100091000	Weak transcription	Lung	lung
17	chr2:100078600-100092200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:100078600-100092600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:100078600-100096800	Weak transcription	NH-A	brain
20	chr2:100078800-100088800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:100078800-100089000	Weak transcription	Ovary	ovary
22	chr2:100078800-100090000	Weak transcription	HUVEC	blood vessel
23	chr2:100078800-100090200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:100078800-100090600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:100078800-100091000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:100078800-100091400	Weak transcription	Adipose Nuclei	Adipose
27	chr2:100078800-100091800	Weak transcription	Fetal Kidney	kidney
28	chr2:100078800-100093200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:100078800-100101400	Weak transcription	Fetal Lung	lung
30	chr2:100078800-100103000	Weak transcription	Primary B cells from cord blood	blood
31	chr2:100078800-100105000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:100079000-100088400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr2:100079000-100090000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:100079000-100091400	Weak transcription	Osteobl	bone
35	chr2:100079000-100091600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:100079200-100088800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:100079200-100088800	Weak transcription	A549	lung
38	chr2:100079200-100090200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:100079200-100091000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:100079200-100091600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:100079200-100092000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:100079200-100092600	Weak transcription	Placenta	Placenta
43	chr2:100079200-100093000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr2:100079200-100096600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:100079200-100098400	Weak transcription	NHDF-Ad	bronchial
46	chr2:100079200-100104000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:100079400-100089000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:100080200-100091000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:100080400-100089400	Weak transcription	Fetal Thymus	thymus
50	chr2:100080400-100090000	Weak transcription	Rectal Mucosa Donor 31	rectum

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