Variant report

Variant	rs6484336
Chromosome Location	chr11:10526622-10526623
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:10517223..10519962-chr11:10526169..10529025,2	MCF-7	breast:
2	chr11:10514613..10516462-chr11:10525360..10527624,2	K562	blood:
3	chr11:10522129..10523861-chr11:10525994..10530069,4	K562	blood:
4	chr11:10521947..10523857-chr11:10526425..10528003,2	K562	blood:
5	chr11:10526046..10528232-chr11:10533609..10536011,2	K562	blood:

Variant related genes	Relation type
ENSG00000133805	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1364738	1.00[CHB][hapmap]
rs1462940	1.00[CHB][hapmap]
rs16908001	1.00[CHB][hapmap]
rs17318955	1.00[CHB][hapmap]
rs17403175	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs17403439	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs17403460	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs17403795	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs17403942	1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs17403977	1.00[CHB][hapmap]
rs1979367	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4025	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs41464450	0.88[CEU][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs4910160	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs55781348	0.80[EUR][1000 genomes]
rs57254418	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv972946	chr11:10523147-10534985	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6484336	OR10A5	cis	cerebellum	SCAN
rs6484336	MICAL2	cis	parietal	SCAN
rs6484336	SNORA45	cis	cerebellum	SCAN
rs6484336	GALNTL4	cis	cerebellum	SCAN
rs6484336	MRVI1	cis	multi-tissue	Pritchard
rs6484336	RNF141	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10495000-10528000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr11:10495200-10530800	Strong transcription	Primary T cells from cord blood	blood
3	chr11:10495800-10529800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:10496600-10529000	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr11:10501600-10550600	Weak transcription	Small Intestine	intestine
6	chr11:10502600-10529000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:10502600-10560800	Weak transcription	Fetal Brain Male	brain
8	chr11:10507800-10544800	Weak transcription	Fetal Kidney	kidney
9	chr11:10510400-10528200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:10510600-10527800	Strong transcription	Thymus	Thymus
11	chr11:10510800-10528400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr11:10511000-10529600	Strong transcription	Fetal Thymus	thymus
13	chr11:10511000-10533200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr11:10512400-10526800	Strong transcription	NHEK	skin
15	chr11:10512800-10526800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:10512800-10531600	Weak transcription	Stomach Mucosa	stomach
17	chr11:10512800-10540400	Weak transcription	Fetal Lung	lung
18	chr11:10512800-10548600	Weak transcription	Right Ventricle	heart
19	chr11:10513000-10526800	Weak transcription	HMEC	breast
20	chr11:10513000-10531800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr11:10513200-10527600	Weak transcription	Right Atrium	heart
22	chr11:10513200-10538000	Weak transcription	Left Ventricle	heart
23	chr11:10513400-10536000	Weak transcription	A549	lung
24	chr11:10513800-10528200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr11:10514000-10527200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:10514200-10529600	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:10514600-10531400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:10514600-10535600	Weak transcription	HSMM	muscle
29	chr11:10514800-10528200	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr11:10515000-10527000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:10515000-10528200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:10515800-10540600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:10516000-10544000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:10517200-10531800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:10520000-10543400	Weak transcription	Colon Smooth Muscle	Colon
36	chr11:10520400-10531600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr11:10521400-10529000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:10522200-10529600	Weak transcription	Fetal Heart	heart
39	chr11:10522200-10531600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:10522200-10531800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:10522200-10541200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:10522400-10532400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr11:10522400-10535600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:10522400-10537800	Weak transcription	Fetal Intestine Large	intestine
45	chr11:10522400-10540600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr11:10522400-10546200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr11:10522400-10560800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr11:10522800-10540600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:10523400-10528400	Strong transcription	Brain Angular Gyrus	brain
50	chr11:10523400-10528400	Strong transcription	K562	blood

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