Variant report

Variant	rs3740690
Chromosome Location	chr11:47188592-47188593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47182976..47185487-chr11:47185518..47189747,4	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11039122	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039131	0.93[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11570094	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs12365578	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12796744	1.00[YRI][hapmap]
rs12803718	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1685404	0.84[CHB][hapmap];0.80[CHD][hapmap]
rs17787966	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs2291119	1.00[YRI][hapmap]
rs2291443	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291444	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2856650	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs7130812	0.85[GIH][hapmap];0.80[MEX][hapmap]
rs752848	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs752850	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7946709	1.00[YRI][hapmap]
rs901750	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3740690	LRP4-AS1	cis	Nerve Tibial	GTEx
rs3740690	PACSIN3	cis	parietal	SCAN
rs3740690	ACP2	cis	lymphoblastoid	seeQTL
rs3740690	MADD	cis	parietal	SCAN
rs3740690	CTD-2384B9.1	cis	Nerve Tibial	GTEx
rs3740690	CKAP5	cis	parietal	SCAN
rs3740690	C1QTNF4	cis	multi-tissue	Pritchard
rs3740690	NUP160	cis	cerebellum	SCAN
rs3740690	LRP4	cis	Nerve Tibial	GTEx
rs3740690	C1QTNF4	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47165400-47188600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:47175200-47188600	Weak transcription	Fetal Heart	heart
3	chr11:47175400-47197600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:47176000-47196600	Strong transcription	Fetal Intestine Small	intestine
5	chr11:47176600-47188600	Weak transcription	Fetal Brain Male	brain
6	chr11:47176800-47193000	Strong transcription	Fetal Brain Female	brain
7	chr11:47176800-47196600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:47178000-47197000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:47178200-47194000	Strong transcription	Dnd41	blood
10	chr11:47178800-47196800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:47180600-47196600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:47180800-47188600	Weak transcription	K562	blood
13	chr11:47181400-47197000	Weak transcription	Right Atrium	heart
14	chr11:47182000-47196400	Strong transcription	Hela-S3	cervix
15	chr11:47182200-47193400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:47182200-47194800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:47182200-47197000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr11:47182400-47196400	Strong transcription	Fetal Intestine Large	intestine
19	chr11:47183200-47194000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr11:47183200-47197000	Strong transcription	Placenta	Placenta
21	chr11:47183200-47197200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:47183400-47190400	Strong transcription	Brain Hippocampus Middle	brain
23	chr11:47183400-47190600	Strong transcription	Gastric	stomach
24	chr11:47183400-47192600	Strong transcription	Primary T cells from cord blood	blood
25	chr11:47183400-47192800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:47183400-47193000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr11:47183400-47193200	Strong transcription	Brain Cingulate Gyrus	brain
28	chr11:47183400-47193800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:47183400-47194600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:47183400-47194600	Strong transcription	Colonic Mucosa	Colon
31	chr11:47183400-47196600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:47183400-47197000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:47183400-47197000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr11:47183400-47197000	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:47183600-47192000	Strong transcription	Primary hematopoietic stem cells	blood
36	chr11:47183600-47192800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:47183600-47193000	Strong transcription	Brain Substantia Nigra	brain
38	chr11:47183600-47193800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:47183600-47194200	Strong transcription	Fetal Thymus	thymus
40	chr11:47183600-47196400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:47183600-47196600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:47183600-47197000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:47183600-47197000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr11:47183800-47196800	Strong transcription	NHLF	lung
45	chr11:47184000-47193000	Strong transcription	Esophagus	oesophagus
46	chr11:47184000-47193600	Strong transcription	Adipose Nuclei	Adipose
47	chr11:47184000-47194000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:47184000-47196800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr11:47184200-47191600	Strong transcription	Right Ventricle	heart
50	chr11:47184200-47196000	Strong transcription	Rectal Mucosa Donor 31	rectum

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