Variant report

Variant	rs4930391
Chromosome Location	chr11:66645254-66645255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66629433..66632533-chr11:66643859..66646288,3	MCF-7	breast:
2	chr11:66632881..66640228-chr11:66642679..66650860,16	MCF-7	breast:
3	chr11:66382271..66386395-chr11:66644556..66647137,4	MCF-7	breast:
4	chr11:66636341..66639567-chr11:66640880..66645266,6	K562	blood:
5	chr11:66644476..66647274-chr11:66681584..66683637,2	MCF-7	breast:
6	chr11:66643151..66645572-chr11:66652641..66654226,2	K562	blood:
7	chr11:66623015..66625016-chr11:66644014..66645662,2	MCF-7	breast:
8	chr11:66611767..66613930-chr11:66642493..66645277,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000173621	Chromatin interaction
ENSG00000199325	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000248643	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12805133	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2276138	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2513658	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3741363	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4930387	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs508443	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs543191	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs569818	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs594313	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs608248	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap]
rs627330	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs682842	0.92[ASW][hapmap];1.00[CEU][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs7107944	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7110302	0.82[CHB][hapmap];0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4930391	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs4930391	ACTN3	cis	Muscle Skeletal	GTEx
rs4930391	SNORA57	cis	cerebellum	SCAN
rs4930391	CCS	cis	lymphoblastoid	seeQTL
rs4930391	EHBP1L1	cis	cerebellum	SCAN
rs4930391	KDM2A	cis	cerebellum	SCAN
rs4930391	CCS	cis	multi-tissue	Pritchard
rs4930391	SYT12	cis	parietal	SCAN
rs4930391	CTSF	cis	multi-tissue	Pritchard
rs4930391	FGF4	cis	parietal	SCAN
rs4930391	LRFN4	cis	multi-tissue	Pritchard
rs4930391	LRFN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66625000-66648800	Weak transcription	Right Atrium	heart
2	chr11:66625400-66645400	Weak transcription	Fetal Lung	lung
3	chr11:66625400-66645800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:66625400-66648000	Weak transcription	Left Ventricle	heart
5	chr11:66625400-66650600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:66625800-66650800	Weak transcription	Osteobl	bone
7	chr11:66627800-66650000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:66629800-66645600	Weak transcription	Pancreas	Pancrea
9	chr11:66630200-66645600	Weak transcription	NHLF	lung
10	chr11:66633600-66648000	Weak transcription	Psoas Muscle	Psoas
11	chr11:66636600-66648000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:66636800-66645600	Weak transcription	Fetal Thymus	thymus
13	chr11:66636800-66646400	Weak transcription	Stomach Mucosa	stomach
14	chr11:66636800-66647800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:66636800-66647800	Weak transcription	Thymus	Thymus
16	chr11:66636800-66648000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:66636800-66650800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:66638000-66650000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr11:66638600-66650200	Weak transcription	Fetal Intestine Large	intestine
20	chr11:66639000-66646600	Weak transcription	Brain Germinal Matrix	brain
21	chr11:66639000-66648000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:66639000-66657200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:66639200-66646000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:66639200-66646200	Weak transcription	Brain Substantia Nigra	brain
25	chr11:66639200-66646400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:66639200-66646600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:66639200-66647800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr11:66639200-66649600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:66639200-66649800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:66639200-66657400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr11:66639400-66645400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:66639400-66645400	Weak transcription	HMEC	breast
33	chr11:66639400-66645600	Weak transcription	Placenta	Placenta
34	chr11:66639400-66645800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:66639400-66645800	Weak transcription	Ovary	ovary
36	chr11:66639400-66646600	Weak transcription	Right Ventricle	heart
37	chr11:66639400-66646600	Weak transcription	Dnd41	blood
38	chr11:66639400-66646800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:66639400-66646800	Weak transcription	Brain Angular Gyrus	brain
40	chr11:66639400-66648000	Weak transcription	Lung	lung
41	chr11:66639400-66648200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:66639400-66650000	Weak transcription	Colonic Mucosa	Colon
43	chr11:66639400-66650400	Weak transcription	Aorta	Aorta
44	chr11:66639400-66659800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:66639600-66645800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:66639600-66647000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr11:66639600-66650200	Weak transcription	Fetal Intestine Small	intestine
48	chr11:66639800-66645600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:66639800-66645600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:66639800-66645600	Weak transcription	NHEK	skin

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