Variant report

Variant	rs17035823
Chromosome Location	chr2:47103998-47103999
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46883974..46884708-chr2:47103987..47104519,2	MCF-7	breast:
2	chr2:47029862..47030805-chr2:47103672..47104853,5	MCF-7	breast:
3	chr2:47102971..47104916-chr2:47106990..47109724,2	K562	blood:
4	chr2:46859559..46860170-chr2:47103480..47104015,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10168851	0.87[ASN][1000 genomes]
rs10190862	0.81[EUR][1000 genomes]
rs10190882	0.81[EUR][1000 genomes]
rs10197474	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11887744	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11898458	1.00[CHB][hapmap]
rs13394007	0.81[EUR][1000 genomes]
rs13410702	0.81[EUR][1000 genomes]
rs13415655	0.81[EUR][1000 genomes]
rs13415771	0.81[EUR][1000 genomes]
rs13419072	0.81[EUR][1000 genomes]
rs13423962	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13432713	0.87[ASN][1000 genomes]
rs17035813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035859	1.00[CEU][hapmap]
rs17035867	1.00[CEU][hapmap]
rs17035884	1.00[CEU][hapmap]
rs17035919	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2017797	0.87[ASN][1000 genomes]
rs2084192	0.81[EUR][1000 genomes]
rs28379847	0.87[ASN][1000 genomes]
rs59191871	0.87[ASN][1000 genomes]
rs60194846	0.81[EUR][1000 genomes]
rs62136788	0.81[EUR][1000 genomes]
rs6714269	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6729120	1.00[CEU][hapmap]
rs6745578	1.00[CEU][hapmap]
rs71423929	0.81[EUR][1000 genomes]
rs720827	0.81[EUR][1000 genomes]
rs7340475	1.00[CEU][hapmap]
rs754411	1.00[CEU][hapmap]
rs7560422	0.87[ASN][1000 genomes]
rs7575172	0.81[EUR][1000 genomes]
rs7595101	0.87[ASN][1000 genomes]
rs8861	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	esv3419289	chr2:47103448-47107046	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3360704	chr2:47103648-47107146	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv3447978	chr2:47103648-47107146	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17035823	MCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47094000-47104200	Weak transcription	Gastric	stomach
2	chr2:47095200-47104200	Weak transcription	Pancreas	Pancrea
3	chr2:47096200-47105000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:47096600-47106400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:47097400-47116200	Enhancers	NHDF-Ad	bronchial
6	chr2:47098800-47106600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:47099600-47106200	Enhancers	Osteobl	bone
8	chr2:47099600-47106800	Enhancers	NHLF	lung
9	chr2:47099800-47106200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr2:47100000-47104600	Enhancers	Colon Smooth Muscle	Colon
11	chr2:47100000-47104600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr2:47100000-47106200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:47100000-47106400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:47100200-47104800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:47100400-47105200	Enhancers	Fetal Heart	heart
16	chr2:47101200-47104200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:47101200-47104200	Weak transcription	Colonic Mucosa	Colon
18	chr2:47101200-47104200	Weak transcription	Fetal Intestine Large	intestine
19	chr2:47101200-47104200	Weak transcription	Fetal Intestine Small	intestine
20	chr2:47101200-47104800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:47101200-47105200	Weak transcription	Brain Angular Gyrus	brain
22	chr2:47101200-47105600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:47101200-47105800	Weak transcription	Brain Anterior Caudate	brain
24	chr2:47101200-47106200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:47101400-47104200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:47101400-47104200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:47101400-47104200	Weak transcription	Esophagus	oesophagus
28	chr2:47101400-47104800	Weak transcription	Spleen	Spleen
29	chr2:47101400-47105400	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:47101400-47106600	Enhancers	Stomach Smooth Muscle	stomach
31	chr2:47101600-47104000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:47101600-47104000	Weak transcription	NHEK	skin
33	chr2:47101600-47104200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:47101600-47104200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:47101600-47104200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:47101600-47104200	Enhancers	A549	lung
37	chr2:47101600-47105400	Weak transcription	Brain Substantia Nigra	brain
38	chr2:47101800-47104000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:47101800-47104200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:47101800-47104200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:47101800-47105600	Weak transcription	HUVEC	blood vessel
42	chr2:47102000-47106400	Enhancers	HepG2	liver
43	chr2:47102200-47104000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:47102200-47104000	Weak transcription	NH-A	brain
45	chr2:47102200-47104200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:47102200-47105800	Enhancers	K562	blood
47	chr2:47102200-47108400	Weak transcription	Adipose Nuclei	Adipose
48	chr2:47102400-47105000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:47102600-47104000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:47102600-47104200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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