Variant report

Variant	rs193718
Chromosome Location	chr5:179409108-179409109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr5:179408708-179409513	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179409014..179411670-chr5:179414218..179416406,2	MCF-7	breast:
2	chr5:179403068..179405769-chr5:179408095..179410312,2	K562	blood:

Variant related genes	Relation type
RNF130	TF binding region
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10061480	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10068039	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10068529	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10078977	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10903246	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs1102190	0.85[ASN][1000 genomes]
rs12153541	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs12653944	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs12656219	0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[TSI][hapmap]
rs173562	0.91[ASN][1000 genomes]
rs185076	0.87[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs248257	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs248258	0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs248315	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248316	0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs248319	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs27013	0.86[CHB][hapmap]
rs27014	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs27016	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs27017	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27019	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs28011	0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs2937020	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35928331	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs394588	0.87[ASN][1000 genomes]
rs4130025	0.83[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs418384	0.85[ASN][1000 genomes]
rs449511	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4700855	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs6871596	0.85[ASN][1000 genomes]
rs6884290	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6888883	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs857181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs857182	0.87[ASN][1000 genomes]
rs857183	0.86[ASN][1000 genomes]
rs857184	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs857189	0.87[ASN][1000 genomes]
rs864137	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs864138	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9329096	0.89[CHD][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs193718	MAML1	cis	cerebellum	SCAN
rs193718	NOP16	cis	parietal	SCAN
rs193718	RASGEF1C	cis	parietal	SCAN
rs193718	RASGEF1C	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179380000-179410800	Weak transcription	Small Intestine	intestine
2	chr5:179381600-179411800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:179389400-179411400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:179392600-179414800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:179396600-179461800	Weak transcription	HSMM	muscle
6	chr5:179400000-179411400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:179400400-179412200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:179401600-179410400	Strong transcription	Primary hematopoietic stem cells	blood
9	chr5:179404400-179421400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:179404600-179410200	Weak transcription	Primary T cells from cord blood	blood
11	chr5:179404600-179439800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:179405200-179409400	Weak transcription	Esophagus	oesophagus
13	chr5:179405200-179410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:179405200-179412200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:179405200-179413600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:179405200-179421800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:179405200-179428200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:179405200-179429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:179405200-179453400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:179405400-179409200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:179405800-179409200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:179405800-179409200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:179405800-179412400	Weak transcription	HSMMtube	muscle
24	chr5:179405800-179414400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:179406000-179409200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:179406000-179410000	Weak transcription	HepG2	liver
27	chr5:179406000-179412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:179406000-179418400	Weak transcription	Fetal Lung	lung
29	chr5:179406000-179428600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:179406200-179409400	Weak transcription	Fetal Intestine Large	intestine
31	chr5:179406200-179411600	Weak transcription	Spleen	Spleen
32	chr5:179406600-179425400	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:179406800-179409200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:179406800-179409400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:179406800-179409800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr5:179406800-179410800	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:179406800-179411400	Weak transcription	Fetal Stomach	stomach
38	chr5:179406800-179421600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:179407000-179409800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:179407000-179428200	Weak transcription	Gastric	stomach
41	chr5:179407200-179409400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr5:179407200-179409400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:179407200-179415000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:179407400-179411400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr5:179407800-179409400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:179407800-179409600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:179407800-179410600	Weak transcription	Brain Anterior Caudate	brain
48	chr5:179407800-179411000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr5:179407800-179412000	Weak transcription	Primary B cells from cord blood	blood
50	chr5:179407800-179413400	Weak transcription	Brain Inferior Temporal Lobe	brain

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