Variant report

Variant	rs6485672
Chromosome Location	chr11:46309968-46309969
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	chr11:46309562..46312239-chr11:46372059..46374065,2	K562	blood:
2	chr11:46295626..46298265-chr11:46308984..46311750,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255007	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10838596	0.88[JPT][hapmap]
rs11038856	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3835060	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6485673	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6485674	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7476	0.88[JPT][hapmap]
rs7943699	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv554201	chr11:46281835-46422686	Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv825867	chr11:46303184-46425613	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6485672	CD82	cis	cerebellum	SCAN
rs6485672	OR4C12	cis	cerebellum	SCAN
rs6485672	API5	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46301400-46311400	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:46303000-46311800	Weak transcription	Hela-S3	cervix
3	chr11:46303400-46310000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:46303600-46311000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:46303600-46311400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr11:46303600-46311600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:46303600-46311600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:46303600-46311800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:46303800-46311600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:46303800-46311800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:46304000-46311200	Weak transcription	Fetal Thymus	thymus
12	chr11:46304200-46311000	Weak transcription	K562	blood
13	chr11:46304400-46311800	Weak transcription	Spleen	Spleen
14	chr11:46307200-46311400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr11:46307200-46317000	Weak transcription	Small Intestine	intestine
16	chr11:46307400-46311000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:46307400-46311200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:46307400-46311400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:46307400-46311400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:46307600-46310200	Weak transcription	Gastric	stomach
21	chr11:46307600-46311000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:46307600-46311000	Weak transcription	NH-A	brain
23	chr11:46307600-46311200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr11:46307600-46311400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr11:46307600-46311400	Weak transcription	Right Atrium	heart
26	chr11:46307600-46311600	Weak transcription	Right Ventricle	heart
27	chr11:46307800-46310000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:46307800-46310000	Weak transcription	Stomach Mucosa	stomach
29	chr11:46307800-46311000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:46307800-46311000	Weak transcription	Fetal Kidney	kidney
31	chr11:46307800-46311200	Weak transcription	Colonic Mucosa	Colon
32	chr11:46307800-46311200	Weak transcription	Fetal Muscle Leg	muscle
33	chr11:46307800-46311200	Weak transcription	Placenta	Placenta
34	chr11:46307800-46311200	Weak transcription	Ovary	ovary
35	chr11:46307800-46311200	Weak transcription	Pancreas	Pancrea
36	chr11:46307800-46311200	Weak transcription	HSMMtube	muscle
37	chr11:46307800-46311400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:46307800-46311400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:46307800-46311400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:46307800-46311600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr11:46308000-46310000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:46308000-46310200	Strong transcription	Fetal Stomach	stomach
43	chr11:46308000-46310600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:46308000-46310800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:46308000-46310800	Weak transcription	Fetal Lung	lung
46	chr11:46308000-46311000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr11:46308000-46311000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr11:46308600-46310200	Weak transcription	NHLF	lung
49	chr11:46308600-46311400	Weak transcription	Left Ventricle	heart
50	chr11:46308800-46310200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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