Variant report

Variant	rs6749689
Chromosome Location	chr2:20396122-20396123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20312716..20316154-chr2:20394135..20396612,3	MCF-7	breast:
2	chr2:20395654..20398324-chr2:20403318..20405686,2	K562	blood:
3	chr2:20393923..20396830-chr2:20398334..20400195,2	K562	blood:
4	chr2:20389942..20391979-chr2:20394528..20396636,2	K562	blood:
5	chr2:20310761..20313054-chr2:20394708..20396754,2	MCF-7	breast:
6	chr2:20396096..20396928-chr2:20424903..20425671,2	MCF-7	breast:
7	chr2:20380951..20386083-chr2:20391129..20397009,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11096646	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11895809	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12615923	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13016862	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2348475	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2348477	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2348478	0.86[ASN][1000 genomes]
rs35363812	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35811865	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35830553	0.85[ASN][1000 genomes]
rs35973557	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36027823	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4350703	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4432408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6742663	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6742681	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6756290	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6749689	MFSD2B	cis	cerebellum	SCAN
rs6749689	MATN3	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20384600-20400000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:20386200-20401400	Weak transcription	Spleen	Spleen
3	chr2:20386600-20401400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:20388600-20400400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:20389200-20413600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:20389400-20398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:20389800-20397600	Weak transcription	Lung	lung
8	chr2:20389800-20400400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:20390600-20400200	Weak transcription	HMEC	breast
10	chr2:20391000-20403600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:20391200-20396400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:20391200-20396800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:20391600-20400400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:20391600-20400600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:20391600-20400600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:20391600-20400800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:20391600-20402400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:20391600-20404800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:20391800-20396200	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:20391800-20398000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:20391800-20398600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:20391800-20400600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:20391800-20402200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:20391800-20423200	Weak transcription	Right Atrium	heart
25	chr2:20392000-20399800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:20392000-20400600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:20392800-20401600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:20393000-20396400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:20394000-20398000	Enhancers	Fetal Lung	lung
30	chr2:20394400-20397200	Enhancers	Fetal Intestine Small	intestine
31	chr2:20394400-20397400	Enhancers	Fetal Intestine Large	intestine
32	chr2:20394400-20400200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:20394600-20396600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:20394600-20398600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:20395200-20396400	Flanking Active TSS	HepG2	liver
36	chr2:20395200-20396800	Enhancers	Pancreas	Pancrea
37	chr2:20395400-20396800	Enhancers	Esophagus	oesophagus
38	chr2:20395400-20397600	Weak transcription	Gastric	stomach
39	chr2:20395400-20399800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:20395600-20400400	Enhancers	Liver	Liver
41	chr2:20395600-20403000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:20395800-20396400	Enhancers	Small Intestine	intestine
43	chr2:20395800-20396600	Enhancers	A549	lung
44	chr2:20395800-20399600	Enhancers	Duodenum Mucosa	Duodenum
45	chr2:20395800-20400800	Enhancers	Stomach Mucosa	stomach
46	chr2:20396000-20396200	Flanking Active TSS	Colonic Mucosa	Colon
47	chr2:20396000-20396400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:20396000-20396400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr2:20396000-20396800	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr2:20396000-20397000	Enhancers	Placenta	Placenta

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