Variant report

Variant	rs11747643
Chromosome Location	chr5:179171834-179171835
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179165749..179167250-chr5:179170923..179173814,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10516140	1.00[JPT][hapmap]
rs11738962	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12654954	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs166624	0.84[JPT][hapmap];0.80[MEX][hapmap]
rs2890060	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4441842	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4504352	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4526069	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4700839	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4701197	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6627	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6871140	0.81[AMR][1000 genomes]
rs6877064	0.85[JPT][hapmap]
rs6879613	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71613416	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7566	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7723450	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9800237	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9800310	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11747643	MAML1	cis	lymphoblastoid	seeQTL
rs11747643	CANX	cis	parietal	SCAN
rs11747643	HRH2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179161000-179174000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:179161000-179174000	Weak transcription	Gastric	stomach
3	chr5:179161000-179174200	Weak transcription	Esophagus	oesophagus
4	chr5:179161000-179181200	Weak transcription	Aorta	Aorta
5	chr5:179161000-179181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:179161000-179181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:179161600-179176600	Weak transcription	HSMMtube	muscle
8	chr5:179161800-179174200	Weak transcription	A549	lung
9	chr5:179161800-179176600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:179161800-179176800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:179161800-179177400	Weak transcription	Fetal Kidney	kidney
12	chr5:179161800-179188800	Weak transcription	NHDF-Ad	bronchial
13	chr5:179162000-179174000	Weak transcription	Liver	Liver
14	chr5:179162000-179176600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:179162000-179176600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:179162000-179176600	Weak transcription	Osteobl	bone
17	chr5:179162000-179176800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:179162000-179181200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:179162000-179181400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:179162000-179181800	Weak transcription	NHLF	lung
21	chr5:179162000-179186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:179162000-179186000	Weak transcription	HSMM	muscle
23	chr5:179162000-179186200	Weak transcription	HMEC	breast
24	chr5:179162000-179186600	Weak transcription	Hela-S3	cervix
25	chr5:179162000-179190400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:179162600-179189000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:179163000-179176600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:179163200-179176600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:179163200-179176800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:179163200-179181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:179163400-179173800	Weak transcription	Brain Hippocampus Middle	brain
32	chr5:179163400-179174000	Weak transcription	Right Atrium	heart
33	chr5:179163400-179174000	Weak transcription	Right Ventricle	heart
34	chr5:179163400-179175600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:179163400-179176600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr5:179163600-179174000	Weak transcription	Small Intestine	intestine
37	chr5:179163800-179180000	Weak transcription	Fetal Brain Male	brain
38	chr5:179164400-179179000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:179164400-179181600	Weak transcription	HUVEC	blood vessel
40	chr5:179164600-179186600	Weak transcription	NH-A	brain
41	chr5:179165000-179174000	Weak transcription	Brain Anterior Caudate	brain
42	chr5:179165000-179176600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:179165000-179176600	Weak transcription	Adipose Nuclei	Adipose
44	chr5:179165000-179176600	Weak transcription	Brain Substantia Nigra	brain
45	chr5:179165000-179176600	Weak transcription	Pancreas	Pancrea
46	chr5:179165000-179181200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr5:179165400-179176600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:179165400-179176800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:179165400-179184600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:179165600-179176800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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