Variant report

Variant	rs4929936
Chromosome Location	chr11:8792622-8792623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8713389..8715952-chr11:8790656..8792768,2	K562	blood:
2	chr11:8708263..8710064-chr11:8790794..8793308,2	MCF-7	breast:
3	chr11:8709572..8711665-chr11:8791796..8793909,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction
ENSG00000254665	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10160684	0.90[CEU][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10500705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10500707	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10522860	0.84[AFR][1000 genomes]
rs10732515	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs10734636	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10734637	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10743087	0.95[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs10743088	0.95[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10743089	0.95[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs10769952	0.88[EUR][1000 genomes]
rs10769953	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10769954	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10769959	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs1079452	0.95[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11042058	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042066	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042068	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11042077	0.90[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs11603335	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2173999	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2292045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292046	0.95[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2873297	0.95[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34090393	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34524863	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34599227	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35098775	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35670750	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763920	0.95[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3812762	0.90[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3842991	0.90[EUR][1000 genomes]
rs3844099	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3844100	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3850933	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3862352	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4929910	0.95[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs4929934	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6484008	0.86[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs6484425	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7120004	0.86[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7934519	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7952335	0.84[CEU][hapmap];0.80[AMR][1000 genomes]
rs905289	0.91[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv553447	chr11:8792622-8825966	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4929936	RPL27A	cis	cerebellum	SCAN
rs4929936	MRPL17	cis	cerebellum	SCAN
rs4929936	STK33	cis	cerebellum	SCAN
rs4929936	SNORA45	cis	cerebellum	SCAN
rs4929936	RPL27A	cis	parietal	SCAN
rs4929936	OR51F1	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8777400-8795800	Enhancers	Rectal Smooth Muscle	rectum
2	chr11:8779600-8799600	Weak transcription	Fetal Brain Male	brain
3	chr11:8781400-8794600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:8784000-8794200	Weak transcription	Colonic Mucosa	Colon
5	chr11:8785200-8799400	Enhancers	Fetal Heart	heart
6	chr11:8786400-8794200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:8786600-8795400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr11:8786600-8795400	Enhancers	Stomach Mucosa	stomach
9	chr11:8786600-8798000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:8786600-8803000	Enhancers	Ovary	ovary
11	chr11:8787000-8797800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:8787600-8795000	Weak transcription	Fetal Intestine Large	intestine
13	chr11:8788200-8794200	Weak transcription	Gastric	stomach
14	chr11:8788200-8797000	Weak transcription	Brain Hippocampus Middle	brain
15	chr11:8788600-8799600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr11:8788800-8792800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr11:8788800-8794200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr11:8788800-8794200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:8788800-8794200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:8788800-8801400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:8788800-8808400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:8789000-8795400	Enhancers	HMEC	breast
23	chr11:8789000-8801200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:8789400-8794800	Weak transcription	Brain Anterior Caudate	brain
25	chr11:8789400-8797000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:8789400-8797400	Weak transcription	Brain Substantia Nigra	brain
27	chr11:8789400-8807600	Weak transcription	Fetal Kidney	kidney
28	chr11:8789600-8799400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:8789600-8805800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:8790200-8793400	Weak transcription	Fetal Intestine Small	intestine
31	chr11:8790400-8793800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:8790400-8794000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:8790400-8794200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:8790400-8795600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr11:8790400-8795800	Weak transcription	Small Intestine	intestine
36	chr11:8790600-8794400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:8790600-8796000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:8790800-8792800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:8790800-8792800	Weak transcription	HUVEC	blood vessel
40	chr11:8790800-8793800	Weak transcription	Placenta	Placenta
41	chr11:8790800-8794000	Weak transcription	Spleen	Spleen
42	chr11:8790800-8794200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:8790800-8794200	Weak transcription	Lung	lung
44	chr11:8790800-8795000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr11:8790800-8797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:8791000-8794400	Weak transcription	Fetal Lung	lung
47	chr11:8791200-8793600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:8791200-8794200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:8791400-8792800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:8791400-8793200	Weak transcription	HSMMtube	muscle

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