Variant report

Variant	rs11729332
Chromosome Location	chr4:7759804-7759805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7733646..7736526-chr4:7759484..7762368,2	K562	blood:

Variant related genes	Relation type
ENSG00000184985	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11721583	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11721609	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs11724632	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs11728778	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11729602	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11730169	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11731942	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs11733311	0.81[EUR][1000 genomes]
rs11734524	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734860	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs11736215	0.88[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs11737447	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113113	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs13117918	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs13125295	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13128495	0.88[CHB][hapmap]
rs13132939	0.83[EUR][1000 genomes]
rs17382379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17382393	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17466895	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34250310	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34276892	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34291966	0.81[EUR][1000 genomes]
rs34352176	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34949259	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35041036	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35161247	0.86[EUR][1000 genomes]
rs35281689	0.81[EUR][1000 genomes]
rs35509185	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35515779	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35592594	0.88[EUR][1000 genomes]
rs35617438	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35668309	0.81[EUR][1000 genomes]
rs35870249	0.88[EUR][1000 genomes]
rs35889107	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3934645	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs41264705	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4443284	0.88[EUR][1000 genomes]
rs4594724	0.87[EUR][1000 genomes]
rs55698135	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55740648	0.81[EUR][1000 genomes]
rs56270003	0.91[EUR][1000 genomes]
rs56352084	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58457272	0.91[EUR][1000 genomes]
rs61036795	0.88[EUR][1000 genomes]
rs62289276	0.91[EUR][1000 genomes]
rs62289280	0.88[EUR][1000 genomes]
rs62291980	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62291982	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62291983	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62291984	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs885260	0.86[EUR][1000 genomes]
rs885261	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][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	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv878575	chr4:7715181-7767755	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv878577	chr4:7757650-7771201	Genic enhancers Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11729332	CLNK	cis	cerebellum	SCAN
rs11729332	AFAP1	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7740200-7765000	Weak transcription	Aorta	Aorta
2	chr4:7740600-7762400	Weak transcription	Pancreas	Pancrea
3	chr4:7746200-7772000	Weak transcription	Brain Anterior Caudate	brain
4	chr4:7747200-7761800	Weak transcription	Colonic Mucosa	Colon
5	chr4:7749400-7760000	Weak transcription	HSMMtube	muscle
6	chr4:7749400-7765600	Weak transcription	Fetal Brain Male	brain
7	chr4:7749400-7767000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:7751800-7761000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:7752800-7767400	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:7753000-7760400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:7753000-7761200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:7753200-7760200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:7753200-7761000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:7754000-7762000	Weak transcription	NHLF	lung
15	chr4:7754200-7765400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:7755400-7763200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:7755400-7768400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:7756000-7761400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:7756000-7766000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:7756200-7762200	Weak transcription	NHEK	skin
21	chr4:7756400-7761400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:7756400-7762200	Weak transcription	HMEC	breast
23	chr4:7756400-7767800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:7756600-7764400	Weak transcription	Esophagus	oesophagus
25	chr4:7756600-7768000	Weak transcription	Brain Angular Gyrus	brain
26	chr4:7757000-7772000	Strong transcription	Brain Germinal Matrix	brain
27	chr4:7757200-7760200	Weak transcription	Fetal Thymus	thymus
28	chr4:7757600-7760000	Genic enhancers	Fetal Muscle Trunk	muscle
29	chr4:7757600-7764400	Strong transcription	NH-A	brain
30	chr4:7757600-7765400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:7757600-7765400	Strong transcription	Osteobl	bone
32	chr4:7757600-7770800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:7757600-7779600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:7757800-7768200	Weak transcription	Fetal Heart	heart
35	chr4:7757800-7768600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:7757800-7772000	Strong transcription	Fetal Intestine Small	intestine
37	chr4:7758000-7760200	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr4:7758000-7762600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:7758000-7780800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr4:7758200-7764600	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr4:7758200-7783200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:7758400-7761000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr4:7758400-7762000	Strong transcription	A549	lung
44	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
45	chr4:7758600-7760000	Enhancers	Rectal Smooth Muscle	rectum
46	chr4:7758600-7760200	Genic enhancers	Fetal Muscle Leg	muscle
47	chr4:7758600-7760400	Enhancers	Left Ventricle	heart
48	chr4:7758600-7760400	Enhancers	HepG2	liver
49	chr4:7758600-7760600	Strong transcription	Fetal Intestine Large	intestine
50	chr4:7758600-7761200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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