Variant report

Variant	rs7629853
Chromosome Location	chr3:179400345-179400346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:179399772..179403297-chr3:179407703..179410091,3	K562	blood:
2	chr3:179399505..179402257-chr3:179403875..179406189,2	K562	blood:
3	chr3:179368925..179372281-chr3:179397125..179401250,3	MCF-7	breast:
4	chr3:179369867..179372337-chr3:179397907..179400346,2	MCF-7	breast:
5	chr3:179399505..179402257-chr3:179403875..179406189,3	K562	blood:

Variant related genes	Relation type
ENSG00000058056	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13097252	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13322033	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13326216	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2268941	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2268942	0.84[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34161332	0.98[ASN][1000 genomes]
rs34197007	0.90[AMR][1000 genomes]
rs35934212	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4854945	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs6771840	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6785332	0.86[CHB][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6788786	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs6797965	0.86[CHB][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6807974	0.88[ASW][hapmap];0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71310390	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9810165	0.88[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9810460	0.88[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9816744	0.80[GIH][hapmap]
rs9859059	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4140	chr3:179383961-179429704	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7629853	MCCC1	cis	cerebellum	SCAN
rs7629853	AP2M1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179372600-179403200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:179372600-179408400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:179372600-179425200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:179374600-179408000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:179376600-179400800	Weak transcription	Dnd41	blood
6	chr3:179380600-179418800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:179384400-179410400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:179384800-179402200	Weak transcription	Fetal Stomach	stomach
9	chr3:179384800-179406200	Weak transcription	HSMM	muscle
10	chr3:179384800-179408000	Weak transcription	Fetal Thymus	thymus
11	chr3:179384800-179415200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:179384800-179425000	Weak transcription	Brain Anterior Caudate	brain
13	chr3:179384800-179428400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:179384800-179443800	Weak transcription	Esophagus	oesophagus
15	chr3:179385000-179415600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:179385000-179439200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:179385000-179448400	Weak transcription	Fetal Brain Male	brain
18	chr3:179385400-179419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:179385600-179405400	Weak transcription	Fetal Brain Female	brain
20	chr3:179390600-179403400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:179390800-179408000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:179391000-179403600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:179391000-179444000	Weak transcription	Pancreas	Pancrea
24	chr3:179391000-179452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:179391400-179403600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:179391400-179404600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:179391400-179415400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:179391400-179426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:179391400-179439200	Weak transcription	NHEK	skin
30	chr3:179391600-179403600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:179391600-179408200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:179391600-179412800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:179391600-179424000	Weak transcription	Hela-S3	cervix
34	chr3:179392600-179425000	Weak transcription	Aorta	Aorta
35	chr3:179394400-179415600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:179394400-179419400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:179396800-179405600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:179396800-179407600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:179397000-179419200	Weak transcription	Liver	Liver
40	chr3:179397200-179423800	Weak transcription	HSMMtube	muscle
41	chr3:179397800-179401000	Enhancers	NHDF-Ad	bronchial
42	chr3:179397800-179439200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:179398000-179403600	Weak transcription	Primary T cells from cord blood	blood
44	chr3:179398000-179403800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:179398200-179400400	Enhancers	Fetal Heart	heart
46	chr3:179398200-179408400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:179398400-179413600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:179398600-179421800	Weak transcription	Brain Substantia Nigra	brain
49	chr3:179398800-179401000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:179398800-179403600	Weak transcription	GM12878-XiMat	blood

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