Variant report

Variant	rs752849
Chromosome Location	chr11:47175327-47175328
allele	A/G
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	CTCF	chr11:47173779-47175556	SK-N-SH	brain:	n/a	chr11:47174815-47174836 chr11:47174822-47174835 chr11:47174820-47174838 chr11:47173836-47173844 chr11:47174821-47174837
2	CTCF	chr11:47175280-47175430	GM12873	blood:	n/a	n/a
3	RAD21	chr11:47173739-47175488	SK-N-SH	brain:	n/a	chr11:47174818-47174837 chr11:47174697-47174709 chr11:47174822-47174836 chr11:47174824-47174833
4	RAD21	chr11:47174458-47175328	HCT-116	colon:	n/a	chr11:47174818-47174837 chr11:47174697-47174709 chr11:47174822-47174836 chr11:47174824-47174833
5	POLR2A	chr11:47173928-47175390	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:47173818-47175361	Hela-S3	cervix:	n/a	n/a
7	SMC3	chr11:47174207-47175551	SK-N-SH	brain:	n/a	chr11:47174380-47174388 chr11:47174822-47174836 chr11:47174557-47174564
8	CTCF	chr11:47175280-47175430	HPAF	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:46867413..46869550-chr11:47174916..47176891,2	K562	blood:
2	chr11:47173854..47175804-chr11:47178111..47180557,3	K562	blood:
3	chr11:46910320..46911827-chr11:47174259..47175968,19	MCF-7	breast:
4	chr11:46910929..46911796-chr11:47174261..47175544,7	MCF-7	breast:
5	chr11:47174410..47175370-chr11:47376484..47377024,2	MCF-7	breast:
6	chr11:46958122..46959949-chr11:47174429..47176046,2	MCF-7	breast:
7	chr11:46910425..46912611-chr11:47175096..47177749,2	K562	blood:

Variant related genes	Relation type
C11orf49	TF binding region
ENSG00000134569	Chromatin interaction
ENSG00000247675	Chromatin interaction
ENSG00000149179	Chromatin interaction
ENSG00000175216	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11039106	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867972	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3740691	0.95[GIH][hapmap]
rs3740694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4752817	0.94[CEU][hapmap]
rs7117590	0.88[ASW][hapmap];0.89[YRI][hapmap]
rs7130989	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7935192	0.88[ASW][hapmap];0.89[YRI][hapmap]
rs7940473	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948786	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs752849	MTCH2	cis	cerebellum	SCAN
rs752849	ARFGAP2	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47160000-47176400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr11:47161600-47176000	Weak transcription	Dnd41	blood
3	chr11:47165000-47184800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:47165000-47185000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:47165200-47185600	Weak transcription	Aorta	Aorta
6	chr11:47165400-47177600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:47165400-47188600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:47165600-47177600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:47165600-47177800	Weak transcription	NHEK	skin
10	chr11:47168600-47177800	Weak transcription	A549	lung
11	chr11:47169200-47176000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:47170800-47176800	Weak transcription	Lung	lung
13	chr11:47171000-47177200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:47171000-47177600	Weak transcription	Esophagus	oesophagus
15	chr11:47171000-47183400	Weak transcription	Gastric	stomach
16	chr11:47171200-47176000	Weak transcription	Fetal Brain Female	brain
17	chr11:47171200-47177600	Weak transcription	Ovary	ovary
18	chr11:47171400-47186000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:47171600-47186400	Weak transcription	Psoas Muscle	Psoas
20	chr11:47173800-47175400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:47173800-47175400	Enhancers	Brain Hippocampus Middle	brain
22	chr11:47173800-47175400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr11:47173800-47175600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:47173800-47175600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:47173800-47176000	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr11:47173800-47176400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr11:47173800-47176800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:47173800-47177000	Enhancers	Fetal Muscle Trunk	muscle
29	chr11:47173800-47178000	Enhancers	Fetal Thymus	thymus
30	chr11:47174000-47175400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:47174000-47175400	Enhancers	Fetal Intestine Small	intestine
32	chr11:47174000-47175400	Enhancers	Pancreas	Pancrea
33	chr11:47174000-47175600	Enhancers	NHDF-Ad	bronchial
34	chr11:47174000-47176000	Enhancers	Primary T cells from cord blood	blood
35	chr11:47174000-47176000	Enhancers	Fetal Muscle Leg	muscle
36	chr11:47174000-47176600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:47174000-47176600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr11:47174000-47176800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr11:47174000-47176800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:47174000-47178000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr11:47174200-47175400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:47174200-47175400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr11:47174200-47175400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr11:47174200-47175400	Enhancers	Adipose Nuclei	Adipose
45	chr11:47174200-47175400	Enhancers	Brain Cingulate Gyrus	brain
46	chr11:47174200-47176000	Enhancers	HSMMtube	muscle
47	chr11:47174200-47176200	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr11:47174200-47176200	Enhancers	NHLF	lung
49	chr11:47174200-47176400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:47174200-47176400	Enhancers	Brain Inferior Temporal Lobe	brain

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