Variant report

Variant	rs1685404
Chromosome Location	chr11:47243665-47243666
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11039122	0.84[CHB][hapmap]
rs11039131	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17787966	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs2013867	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs2167079	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs2291119	0.88[CEU][hapmap]
rs2291443	0.84[CHB][hapmap]
rs2291444	0.84[CHB][hapmap]
rs326217	0.88[CEU][hapmap]
rs326222	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs3758673	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs7120118	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs7395581	0.82[JPT][hapmap]
rs752848	0.84[CHB][hapmap]
rs752850	0.84[CHB][hapmap]
rs830085	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs901746	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs901750	0.84[CHB][hapmap];0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1685404	MTCH2	cis	cerebellum	SCAN
rs1685404	C1QTNF4	cis	multi-tissue	Pritchard
rs1685404	MYBPC3	cis	multi-tissue	Pritchard
rs1685404	PACSIN3	cis	cerebellum	SCAN
rs1685404	NR1H3	cis	cerebellum	SCAN
rs1685404	MADD	cis	cerebellum	SCAN
rs1685404	Hs.6637	cis	multi-tissue	Pritchard
rs1685404	LRP4	cis	Nerve Tibial	GTEx
rs1685404		cis	Lymphoblastoid	GTEx
rs1685404	OR4B1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238400-47245000	Weak transcription	Fetal Kidney	kidney
2	chr11:47238400-47246200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr11:47238400-47246600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:47238400-47255800	Weak transcription	Brain Anterior Caudate	brain
5	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:47238600-47243800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr11:47238600-47245600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:47238600-47247600	Weak transcription	Colonic Mucosa	Colon
9	chr11:47238600-47253800	Weak transcription	Aorta	Aorta
10	chr11:47238600-47254200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:47238600-47255400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:47238600-47255400	Weak transcription	Right Ventricle	heart
13	chr11:47238600-47255600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:47238600-47255800	Weak transcription	Brain Substantia Nigra	brain
15	chr11:47238600-47255800	Weak transcription	Right Atrium	heart
16	chr11:47238600-47256000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:47238600-47259600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:47238600-47261000	Weak transcription	Small Intestine	intestine
19	chr11:47238800-47244000	Weak transcription	Placenta	Placenta
20	chr11:47238800-47254000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:47239000-47244800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:47239400-47244400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr11:47239400-47245000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:47239400-47246200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr11:47239400-47252200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:47239400-47252200	Strong transcription	Fetal Thymus	thymus
27	chr11:47239400-47255000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr11:47239600-47245600	Strong transcription	Thymus	Thymus
29	chr11:47239600-47251800	Strong transcription	Fetal Stomach	stomach
30	chr11:47239800-47245600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr11:47239800-47245600	Strong transcription	Fetal Intestine Small	intestine
32	chr11:47239800-47247400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:47239800-47254200	Weak transcription	Lung	lung
34	chr11:47239800-47255600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:47239800-47255600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr11:47240000-47245600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr11:47240000-47247200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr11:47240000-47252400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr11:47240000-47260200	Weak transcription	Fetal Brain Female	brain
40	chr11:47240200-47244000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr11:47240200-47245600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr11:47240200-47254200	Weak transcription	Esophagus	oesophagus
43	chr11:47240200-47254200	Weak transcription	Stomach Mucosa	stomach
44	chr11:47240200-47254600	Weak transcription	Pancreas	Pancrea
45	chr11:47240200-47255400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr11:47240200-47255600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr11:47240200-47255800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr11:47240200-47256000	Weak transcription	Gastric	stomach
49	chr11:47240200-47266600	Weak transcription	Fetal Brain Male	brain
50	chr11:47240400-47246000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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