Variant report

Variant	rs11824
Chromosome Location	chr3:111836566-111836567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10934145	0.88[CEU][hapmap]
rs11707558	0.88[CEU][hapmap]
rs11922559	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs12488760	0.88[CEU][hapmap]
rs12634769	0.88[CEU][hapmap]
rs13066495	0.85[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs13074229	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13081485	0.80[CEU][hapmap]
rs13081935	0.81[CEU][hapmap]
rs13082509	0.81[CEU][hapmap]
rs13087086	0.81[CEU][hapmap]
rs13091454	0.82[CEU][hapmap]
rs13100724	0.81[CEU][hapmap]
rs2120095	0.81[CEU][hapmap]
rs340163	0.89[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs340165	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340172	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234412	0.88[CEU][hapmap]
rs4234413	0.88[CEU][hapmap]
rs4282033	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs4392388	0.88[CEU][hapmap]
rs4401342	0.88[CEU][hapmap]
rs4505669	0.88[CEU][hapmap]
rs4560270	0.87[CEU][hapmap]
rs4572740	0.81[CEU][hapmap]
rs4585166	0.81[CEU][hapmap]
rs4632517	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs4682097	0.87[CEU][hapmap]
rs4682355	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[ASN][1000 genomes]
rs4682357	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682380	0.88[CEU][hapmap]
rs6773916	0.92[CEU][hapmap]
rs6781344	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs6798551	0.88[CEU][hapmap]
rs729641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746026	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs746027	0.82[EUR][1000 genomes]
rs7613061	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs7616261	0.88[CEU][hapmap]
rs7624367	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs7638520	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs923745	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9758396	0.88[CEU][hapmap]
rs9809384	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs9809404	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs9822786	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs9823421	0.88[CEU][hapmap]
rs9826043	0.88[CEU][hapmap]
rs9847574	0.86[CEU][hapmap]
rs9860819	0.88[CEU][hapmap]
rs9863061	0.84[CEU][hapmap]
rs9878213	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs9879184	0.88[CEU][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11824	SLC9A10	cis	parietal	SCAN
rs11824	GCET2	cis	parietal	SCAN
rs11824	CD200	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111810400-111852000	Weak transcription	Esophagus	oesophagus
2	chr3:111812000-111844000	Weak transcription	Colonic Mucosa	Colon
3	chr3:111812000-111845600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:111812200-111853000	Weak transcription	Right Ventricle	heart
5	chr3:111812600-111840200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:111819000-111840400	Weak transcription	Fetal Stomach	stomach
7	chr3:111819600-111847800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:111821200-111843600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:111821400-111839000	Weak transcription	Osteobl	bone
10	chr3:111821400-111843600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:111822000-111844600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:111822400-111839200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:111823400-111837800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:111825600-111838600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:111825800-111844400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:111827000-111838600	Weak transcription	Spleen	Spleen
17	chr3:111828200-111838600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:111828400-111838200	Weak transcription	Stomach Mucosa	stomach
19	chr3:111830000-111837800	Strong transcription	NHEK	skin
20	chr3:111830600-111853200	Weak transcription	Lung	lung
21	chr3:111830800-111845400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:111831200-111837400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:111831200-111838800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:111831400-111843000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:111832000-111844600	Weak transcription	Hela-S3	cervix
26	chr3:111832400-111838600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:111832400-111840600	Enhancers	Primary B cells from cord blood	blood
28	chr3:111832600-111841600	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:111833000-111838600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:111833200-111837600	Weak transcription	HMEC	breast
31	chr3:111833200-111838400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:111833200-111844000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:111833600-111839600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:111833800-111838600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr3:111834200-111836800	Genic enhancers	Fetal Thymus	thymus
36	chr3:111834200-111838200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:111834200-111853800	Weak transcription	Fetal Intestine Small	intestine
38	chr3:111834400-111838400	Weak transcription	HSMM	muscle
39	chr3:111834400-111838800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:111834400-111848000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:111834600-111837800	Flanking Active TSS	GM12878-XiMat	blood
42	chr3:111834600-111841600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:111834800-111838600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:111834800-111838600	Weak transcription	HSMMtube	muscle
45	chr3:111835200-111840800	Strong transcription	NH-A	brain
46	chr3:111835400-111837600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:111835600-111836800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:111835600-111836800	Genic enhancers	Thymus	Thymus
49	chr3:111835600-111837800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:111835600-111839000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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