Variant report

Variant	rs1647405
Chromosome Location	chr11:57477889-57477890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:57477445-57477951	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57416825..57418474-chr11:57477020..57479617,2	K562	blood:
2	chr11:57477767..57479895-chr11:57568305..57570936,2	K562	blood:
3	chr11:57433212..57437810-chr11:57477098..57481918,8	MCF-7	breast:
4	chr11:57459870..57462694-chr11:57476257..57478537,2	MCF-7	breast:
5	chr11:57447901..57451282-chr11:57477513..57480655,3	K562	blood:
6	chr11:57433884..57439071-chr11:57477629..57483930,15	K562	blood:

No data

Variant related genes	Relation type
TMX2	TF binding region
TMX2-CTNND1	TF binding region
ENSG00000198561	Chromatin interaction
ENSG00000166793	Chromatin interaction
ENSG00000156599	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10792112	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896633	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896636	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896647	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11229066	1.00[JPT][hapmap]
rs11229067	1.00[JPT][hapmap]
rs11229113	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229116	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229130	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229131	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229148	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11570190	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11601320	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11601449	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11602109	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11603020	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs11604325	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11604333	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11605731	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11606396	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11606677	1.00[JPT][hapmap]
rs11607056	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146541	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12362166	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12785533	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12790196	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12804972	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12805841	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12807250	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17455520	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2081361	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2847308	1.00[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];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926656	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35808061	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781885	0.89[EUR][1000 genomes]
rs3824988	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4827	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs488769	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4926	1.00[JPT][hapmap]
rs499188	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527528	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs543725	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs547891	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591434	0.80[ASN][1000 genomes]
rs682503	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs708228	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7116341	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7117205	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs7117878	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7121169	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7129727	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71484461	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71484468	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs731384	0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs7932091	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7936998	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7938083	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7949841	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9420	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv975360	chr11:57466716-57480320	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1647405	OR5T1	cis	cerebellum	SCAN
rs1647405	LRRC55	cis	parietal	SCAN
rs1647405	MS4A7	cis	parietal	SCAN
rs1647405	MED19	cis	cerebellum	SCAN
rs1647405	OR4D10	cis	parietal	SCAN
rs1647405	MED19	Cis_1M	lymphoblastoid	RTeQTL
rs1647405	TIMM10	cis	parietal	SCAN
rs1647405	PRG3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57436600-57479000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57438600-57478200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:57461400-57478400	Weak transcription	Fetal Heart	heart
4	chr11:57464400-57478800	Weak transcription	Psoas Muscle	Psoas
5	chr11:57467600-57478200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:57468400-57478400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:57468400-57478800	Weak transcription	Right Ventricle	heart
8	chr11:57469200-57478800	Weak transcription	Ovary	ovary
9	chr11:57469400-57478800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:57471400-57478000	Weak transcription	Primary B cells from cord blood	blood
11	chr11:57471800-57478400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:57472000-57478400	Weak transcription	Fetal Kidney	kidney
13	chr11:57472000-57478600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:57472000-57478600	Weak transcription	Small Intestine	intestine
15	chr11:57472200-57478400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:57472200-57478400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:57472400-57478000	Weak transcription	Hela-S3	cervix
18	chr11:57472400-57478400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:57472400-57478400	Weak transcription	Brain Angular Gyrus	brain
20	chr11:57472600-57478000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:57472600-57478000	Weak transcription	HSMM	muscle
22	chr11:57472600-57478200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:57472600-57478200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr11:57472600-57478200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:57472600-57478200	Weak transcription	Gastric	stomach
26	chr11:57472600-57478400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr11:57472600-57478400	Weak transcription	Brain Substantia Nigra	brain
28	chr11:57472600-57478400	Weak transcription	NHEK	skin
29	chr11:57472600-57478600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr11:57472600-57478600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:57472600-57478600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr11:57472600-57478600	Weak transcription	NH-A	brain
33	chr11:57472600-57478800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:57472600-57478800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:57472600-57478800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr11:57472600-57478800	Weak transcription	Aorta	Aorta
37	chr11:57472800-57478200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:57472800-57478200	Weak transcription	Brain Germinal Matrix	brain
39	chr11:57472800-57478200	Weak transcription	Colonic Mucosa	Colon
40	chr11:57472800-57478200	Weak transcription	Left Ventricle	heart
41	chr11:57472800-57478200	Weak transcription	NHLF	lung
42	chr11:57472800-57478400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:57472800-57478400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr11:57472800-57478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:57472800-57478400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:57472800-57478600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr11:57472800-57478600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:57472800-57478600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:57472800-57478600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:57472800-57478600	Weak transcription	Primary B cells from peripheral blood	blood

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