Variant report

Variant	rs277638
Chromosome Location	chr3:100079447-100079448
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:100079210-100079747	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr3:100079223-100080512	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr3:100079309-100080908	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr3:100079364-100079983	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:100078299-100082124	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:100079202-100079499	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:100077324-100082038	K562	blood:	n/a	n/a
8	POLR2A	chr3:100079393-100079505	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100079303..100082344-chr3:100118989..100121864,3	K562	blood:

Variant related genes	Relation type
ENSG00000273488	TF binding region
ENSG00000206535	Chromatin interaction
ENSG00000154174	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1045206	0.82[YRI][hapmap]
rs10936180	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1123578	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1214375	0.86[YRI][hapmap]
rs1214377	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1214380	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1214381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1228184	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12495001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1530283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs166747	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2316701	0.83[YRI][hapmap]
rs277620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277622	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs277623	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277626	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277628	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs277629	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277630	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277635	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277639	0.82[MEX][hapmap]
rs277641	0.82[MEX][hapmap]
rs277642	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277644	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277651	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs372438	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772692	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs392066	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs402870	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs413425	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs431069	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs432715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6780662	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs6791102	0.90[ASN][1000 genomes]
rs6794955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7616634	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7641630	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
5	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:100069400-100082400	Weak transcription	Fetal Brain Male	brain
8	chr3:100069600-100080600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:100069600-100083800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:100069600-100085800	Weak transcription	Small Intestine	intestine
11	chr3:100069600-100087000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:100071000-100080800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:100071000-100087800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:100071000-100087800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:100071000-100093600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:100071000-100103200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:100071000-100104400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:100071200-100080800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:100071200-100081000	Strong transcription	A549	lung
20	chr3:100071400-100082200	Strong transcription	NHEK	skin
21	chr3:100071400-100088000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:100071400-100105800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:100071600-100079600	Weak transcription	Fetal Kidney	kidney
24	chr3:100071600-100080800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:100071600-100087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:100071800-100084200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:100071800-100090600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:100072000-100084200	Weak transcription	K562	blood
29	chr3:100072200-100080600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:100072200-100081000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:100072200-100081000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:100072400-100080200	Weak transcription	HUVEC	blood vessel
33	chr3:100072400-100080800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:100072600-100084800	Weak transcription	Hela-S3	cervix
35	chr3:100073200-100079600	Weak transcription	Fetal Lung	lung
36	chr3:100073200-100080800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:100073200-100082400	Weak transcription	NHLF	lung
38	chr3:100073200-100090200	Weak transcription	Esophagus	oesophagus
39	chr3:100073400-100090400	Weak transcription	Pancreas	Pancrea
40	chr3:100073400-100096400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:100073800-100080000	Weak transcription	Aorta	Aorta
42	chr3:100073800-100090600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:100073800-100098200	Weak transcription	Gastric	stomach
44	chr3:100074000-100080800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:100074000-100083200	Weak transcription	Colonic Mucosa	Colon
46	chr3:100074000-100084000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:100074400-100079600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:100074400-100083800	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:100074600-100080200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:100074600-100080200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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