Variant report

Variant	rs11944122
Chromosome Location	chr4:442021-442022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11945320	0.89[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs4690261	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61793705	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1001899	chr4:68809-517736	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv1010829	chr4:147570-547070	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv536970	chr4:147570-547070	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11944122	GAK	cis	cerebellum	SCAN
rs11944122	ZNF595	cis	parietal	SCAN
rs11944122	ABCA11P	cis	parietal	SCAN
rs11944122	ZNF721	cis	parietal	SCAN
rs11944122	ZNF141	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:395000-455800	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr4:405000-455400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:407600-466200	ZNF genes & repeats	Liver	Liver
4	chr4:414800-454200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr4:415600-455200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:416000-455200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:416400-466800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:416600-455200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
9	chr4:418800-444200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:419600-455200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
11	chr4:419600-455200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
12	chr4:419800-455200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:423400-453800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
14	chr4:423400-455200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
15	chr4:423600-455000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr4:423600-455200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr4:423800-449400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:423800-455200	ZNF genes & repeats	Dnd41	blood
19	chr4:425400-449800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
20	chr4:425400-465400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
21	chr4:433400-466400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
22	chr4:433400-467000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:434200-442200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:434600-454000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr4:435000-449400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:435000-449800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:435400-449400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
28	chr4:435600-449800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
29	chr4:435600-466000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
30	chr4:435800-444600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr4:435800-449000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr4:435800-455200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
33	chr4:436400-442600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
34	chr4:436600-466000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:437000-455000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
36	chr4:437000-455200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:437200-442400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:437400-454400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
39	chr4:438800-443400	Weak transcription	NH-A	brain
40	chr4:438800-445000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:439200-445000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:439600-442200	ZNF genes & repeats	Fetal Lung	lung
43	chr4:439600-449800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:440400-442200	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr4:441000-442600	Strong transcription	Primary B cells from cord blood	blood
46	chr4:441000-445200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:441200-444400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:441200-444400	Weak transcription	Esophagus	oesophagus
49	chr4:441400-446600	Weak transcription	Hela-S3	cervix
50	chr4:441600-443000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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