Variant report

Variant	rs3772000
Chromosome Location	chr2:7113332-7113333
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	chr2:7113332..7116286-chr2:9136805..9139495,2	MCF-7	breast:
2	chr2:7065097..7066741-chr2:7112184..7114861,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11685858	0.81[CEU][hapmap];0.80[GIH][hapmap]
rs1448869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1448870	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2166967	0.84[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34393586	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3771999	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669122	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669123	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55736658	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs771254	0.95[JPT][hapmap]
rs771272	0.81[CEU][hapmap];0.80[GIH][hapmap]
rs881938	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv833326	chr2:6985027-7142564	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv2598	chr2:7088737-7133415	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3772000	ADAM17	cis	cerebellum	SCAN
rs3772000	RNF144A	cis	cerebellum	SCAN
rs3772000	TSSC1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7079000-7113400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:7083800-7129600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:7084200-7122200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:7085000-7120200	Weak transcription	Fetal Intestine Small	intestine
5	chr2:7096800-7120600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:7097200-7126200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:7098000-7115800	Weak transcription	HepG2	liver
8	chr2:7099000-7123600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:7101000-7113400	Weak transcription	NHDF-Ad	bronchial
10	chr2:7101000-7117400	Weak transcription	Right Atrium	heart
11	chr2:7101000-7130000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:7101200-7114000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:7101200-7116000	Weak transcription	Gastric	stomach
14	chr2:7101200-7117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:7101200-7126200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:7101200-7144000	Weak transcription	Aorta	Aorta
17	chr2:7101200-7154000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:7101400-7117200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:7101600-7117200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:7101800-7126200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:7102000-7117400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:7102200-7117400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:7102400-7117000	Weak transcription	Fetal Brain Male	brain
24	chr2:7104200-7120600	Strong transcription	Dnd41	blood
25	chr2:7105600-7120600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:7106200-7123200	Strong transcription	Primary T cells from cord blood	blood
27	chr2:7107200-7117000	Weak transcription	Fetal Lung	lung
28	chr2:7108800-7115400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:7109000-7114600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:7109200-7113600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:7109200-7115800	Weak transcription	Left Ventricle	heart
32	chr2:7109200-7116000	Weak transcription	Fetal Heart	heart
33	chr2:7109200-7117400	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:7109200-7137000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:7109400-7117400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:7109800-7116000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:7110400-7113400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr2:7110400-7114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:7110600-7120200	Weak transcription	Fetal Thymus	thymus
40	chr2:7110800-7114000	Strong transcription	Fetal Stomach	stomach
41	chr2:7110800-7115000	Enhancers	Brain Substantia Nigra	brain
42	chr2:7111000-7113400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:7111000-7113600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:7111000-7115400	Weak transcription	Esophagus	oesophagus
45	chr2:7111000-7118000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:7111200-7117000	Weak transcription	Brain Germinal Matrix	brain
47	chr2:7111200-7117200	Weak transcription	Fetal Brain Female	brain
48	chr2:7111400-7113600	Weak transcription	Pancreas	Pancrea
49	chr2:7111600-7126400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr2:7111800-7113600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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