Variant report

Variant	rs28011
Chromosome Location	chr5:179407229-179407230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10903246	0.85[CHD][hapmap]
rs12653944	0.82[CHD][hapmap]
rs193718	0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs248316	0.83[CHD][hapmap]
rs27014	0.85[CHD][hapmap]
rs27016	0.85[CHD][hapmap]
rs27017	0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs449511	0.85[CHD][hapmap]
rs4700705	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs495267	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][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	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
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28011	TRIM7	cis	parietal	SCAN
rs28011	DOK3	cis	cerebellum	SCAN
rs28011	RASGEF1C	cis	cerebellum	SCAN
rs28011	RASGEF1C	cis	parietal	SCAN
rs28011	LMAN2	cis	cerebellum	SCAN
rs28011	LOC202181	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179380000-179410800	Weak transcription	Small Intestine	intestine
2	chr5:179381000-179407800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:179381600-179411800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:179383200-179408600	Weak transcription	A549	lung
5	chr5:179389400-179411400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:179392600-179414800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:179396600-179461800	Weak transcription	HSMM	muscle
8	chr5:179399000-179408000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:179399000-179408400	Strong transcription	Brain Germinal Matrix	brain
10	chr5:179399400-179408000	Strong transcription	Left Ventricle	heart
11	chr5:179399400-179408200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr5:179399800-179408400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:179400000-179408400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:179400000-179411400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr5:179400200-179408200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:179400200-179408400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:179400400-179407400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr5:179400400-179408000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr5:179400400-179408400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:179400400-179412200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr5:179400600-179408200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:179400600-179408200	Strong transcription	Lung	lung
23	chr5:179400600-179408400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:179400800-179408000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:179400800-179408000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:179401000-179407800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:179401200-179407800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:179401400-179408000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:179401600-179410400	Strong transcription	Primary hematopoietic stem cells	blood
30	chr5:179402000-179408200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:179402000-179409000	Weak transcription	Fetal Kidney	kidney
32	chr5:179402600-179407600	Strong transcription	Fetal Brain Female	brain
33	chr5:179402600-179407800	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr5:179402600-179408000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:179402800-179407800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:179402800-179407800	Strong transcription	Brain Anterior Caudate	brain
37	chr5:179402800-179408200	Weak transcription	Fetal Brain Male	brain
38	chr5:179402800-179408600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:179402800-179409000	Weak transcription	Colonic Mucosa	Colon
40	chr5:179403000-179407800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:179403400-179407800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:179403400-179407800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr5:179403600-179407800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:179403800-179408000	Strong transcription	Brain Hippocampus Middle	brain
45	chr5:179404400-179421400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr5:179404600-179410200	Weak transcription	Primary T cells from cord blood	blood
47	chr5:179404600-179439800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:179404800-179407800	Strong transcription	Primary B cells from cord blood	blood
49	chr5:179405200-179408400	Weak transcription	Brain Angular Gyrus	brain
50	chr5:179405200-179408400	Weak transcription	Placenta	Placenta

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