Variant report

Variant	rs11725167
Chromosome Location	chr4:166194363-166194364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10517833	0.84[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs11725104	1.00[JPT][hapmap]
rs11729242	1.00[JPT][hapmap]
rs16999615	0.85[CEU][hapmap]
rs17009130	1.00[JPT][hapmap]
rs17488289	0.84[EUR][1000 genomes]
rs17488436	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs17585396	0.84[CEU][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs17585515	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs17585550	0.84[CEU][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs17842697	0.85[CEU][hapmap]
rs17842699	0.85[CEU][hapmap]
rs1818471	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs2048604	0.88[CEU][hapmap]
rs28472332	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55648903	0.83[EUR][1000 genomes]
rs55650232	0.87[EUR][1000 genomes]
rs55705752	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55806488	0.88[EUR][1000 genomes]
rs56104713	0.84[EUR][1000 genomes]
rs56287687	0.91[EUR][1000 genomes]
rs56407727	0.91[EUR][1000 genomes]
rs56410965	0.83[EUR][1000 genomes]
rs58426709	0.81[EUR][1000 genomes]
rs58781490	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67414450	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6830714	0.85[CEU][hapmap]
rs6831119	0.88[EUR][1000 genomes]
rs6853219	0.90[EUR][1000 genomes]
rs72699595	0.83[EUR][1000 genomes]
rs72699598	0.83[EUR][1000 genomes]
rs72701606	0.90[EUR][1000 genomes]
rs72701616	0.83[EUR][1000 genomes]
rs7676311	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685245	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv881168	chr4:165975122-166196438	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv980272	chr4:166179748-166197533	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11725167	INTS12	trans	cerebellum	SCAN
rs11725167	NAF1	cis	parietal	SCAN
rs11725167	KLHL2	cis	Artery Tibial	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166129600-166196800	Weak transcription	Pancreas	Pancrea
2	chr4:166130600-166200800	Weak transcription	Lung	lung
3	chr4:166131600-166196800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:166144600-166218800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:166156200-166199200	Weak transcription	Ovary	ovary
6	chr4:166170000-166210000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:166170600-166209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:166177000-166196000	Weak transcription	Gastric	stomach
9	chr4:166177200-166218800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:166177400-166199200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:166177400-166201200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:166177400-166201600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:166177400-166204200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:166177400-166209200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:166177400-166215200	Weak transcription	Fetal Stomach	stomach
16	chr4:166177400-166216000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:166177400-166218600	Weak transcription	Spleen	Spleen
18	chr4:166177400-166219000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:166177600-166194400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:166177800-166205000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:166178200-166194600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:166178400-166205600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:166178800-166194600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:166178800-166197200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:166178800-166200600	Weak transcription	Fetal Intestine Large	intestine
26	chr4:166178800-166207600	Weak transcription	Primary B cells from cord blood	blood
27	chr4:166178800-166209200	Weak transcription	Brain Substantia Nigra	brain
28	chr4:166178800-166209400	Weak transcription	Brain Anterior Caudate	brain
29	chr4:166178800-166218800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:166178800-166218800	Weak transcription	Esophagus	oesophagus
31	chr4:166180200-166194600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:166181200-166199200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:166181200-166204600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:166181200-166208200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:166181400-166194400	Weak transcription	Dnd41	blood
36	chr4:166182200-166196000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:166182200-166207000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr4:166182800-166207800	Weak transcription	Primary T cells from cord blood	blood
39	chr4:166183600-166209200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:166183800-166196600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr4:166183800-166207000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:166183800-166209600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:166183800-166215200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:166183800-166218800	Weak transcription	Aorta	Aorta
45	chr4:166184200-166202400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:166184800-166200600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:166185600-166194400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:166185600-166198800	Weak transcription	Liver	Liver
49	chr4:166185800-166197000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:166189000-166200800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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