Variant report

Variant	rs401514
Chromosome Location	chr3:155591933-155591934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:155461486..155465793-chr3:155586998..155592801,6	K562	blood:
2	chr3:155568718..155574348-chr3:155586235..155593210,15	K562	blood:
3	chr3:155522036..155526613-chr3:155586597..155592084,8	K562	blood:
4	chr3:155508129..155511910-chr3:155589025..155592150,5	K562	blood:
5	chr3:155587045..155589767-chr3:155590571..155592335,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169359	Chromatin interaction
ENSG00000114805	Chromatin interaction
ENSG00000174928	Chromatin interaction
ENSG00000163655	Chromatin interaction
ENSG00000214919	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10936021	0.88[AFR][1000 genomes]
rs11712694	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634282	0.88[AFR][1000 genomes]
rs12636569	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12638792	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12638836	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356252	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1711084	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1878211	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2067877	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2320318	0.96[EUR][1000 genomes]
rs28438758	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2874232	0.86[AFR][1000 genomes]
rs3772112	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406701	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445758	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4679757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680222	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519400	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60788059	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6441022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441023	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[GIH][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441024	0.85[AFR][1000 genomes]
rs6766927	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775044	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777776	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6797289	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6806109	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs819844	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs819858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs843931	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9820534	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825321	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9846097	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9866164	0.81[ASN][1000 genomes]
rs9875112	0.84[EUR][1000 genomes]
rs9883153	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753744	chr3:155487298-155707298	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
3	nsv877681	chr3:155535670-155654017	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155589600-155599600	Weak transcription	Spleen	Spleen
2	chr3:155589800-155592800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:155589800-155596600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:155589800-155596600	Weak transcription	Lung	lung
5	chr3:155589800-155607000	Weak transcription	Pancreas	Pancrea
6	chr3:155590000-155592800	Weak transcription	Aorta	Aorta
7	chr3:155590000-155592800	Weak transcription	Psoas Muscle	Psoas
8	chr3:155590000-155593000	Weak transcription	Gastric	stomach
9	chr3:155590000-155599400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:155590200-155592600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:155590200-155592800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:155590200-155592800	Weak transcription	Ovary	ovary
13	chr3:155590200-155593000	Weak transcription	Left Ventricle	heart
14	chr3:155590200-155593000	Weak transcription	Right Atrium	heart
15	chr3:155590200-155594000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:155590200-155596600	Weak transcription	Thymus	Thymus
17	chr3:155590200-155599000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:155590200-155599400	Weak transcription	Right Ventricle	heart
19	chr3:155590200-155608400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:155590200-155643000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:155590200-155667400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:155590400-155592800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:155590400-155592800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:155590400-155593200	Weak transcription	Fetal Heart	heart
25	chr3:155590400-155593800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:155590400-155594200	Weak transcription	Fetal Stomach	stomach
27	chr3:155590400-155594800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:155590400-155596600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:155590600-155592000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:155590600-155593000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:155590600-155597800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:155590800-155592000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:155590800-155592000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:155590800-155592000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:155590800-155592800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:155590800-155593200	Weak transcription	Fetal Brain Female	brain
37	chr3:155590800-155593800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:155590800-155593800	Weak transcription	Fetal Brain Male	brain
39	chr3:155590800-155607200	Weak transcription	Brain Angular Gyrus	brain
40	chr3:155591000-155592000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:155591000-155592000	Weak transcription	A549	lung
42	chr3:155591000-155592200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:155591000-155592400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr3:155591000-155592400	Weak transcription	NH-A	brain
45	chr3:155591000-155593200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:155591000-155593200	Weak transcription	Osteobl	bone
47	chr3:155591000-155593400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:155591000-155593800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:155591000-155594000	Weak transcription	Brain Anterior Caudate	brain
50	chr3:155591000-155594000	Weak transcription	HSMM	muscle

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