Variant report

Variant	rs13423962
Chromosome Location	chr2:47180609-47180610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47179225..47182053-chr2:47271566..47273267,2	K562	blood:
2	chr2:47167363..47169849-chr2:47180140..47182205,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10164756	0.87[CEU][hapmap]
rs10168851	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174894	0.87[EUR][1000 genomes]
rs10199965	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11887744	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11894319	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11897050	0.87[CEU][hapmap]
rs11898458	1.00[CHB][hapmap]
rs13388612	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13391660	0.87[CEU][hapmap]
rs13406024	0.87[CEU][hapmap]
rs13417753	0.87[CEU][hapmap]
rs13424086	0.87[CEU][hapmap]
rs13432713	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035813	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17035823	0.87[ASN][1000 genomes]
rs17035878	0.87[CEU][hapmap]
rs17035887	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17035912	0.87[CEU][hapmap]
rs17035919	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2017797	1.00[ASN][1000 genomes]
rs2289927	0.87[EUR][1000 genomes]
rs2289928	0.87[EUR][1000 genomes]
rs28379847	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28516550	0.87[EUR][1000 genomes]
rs4300885	0.87[CEU][hapmap]
rs59191871	1.00[ASN][1000 genomes]
rs62136823	0.87[EUR][1000 genomes]
rs62136825	0.87[EUR][1000 genomes]
rs62136827	0.83[EUR][1000 genomes]
rs62140550	0.89[EUR][1000 genomes]
rs6706031	0.87[EUR][1000 genomes]
rs6714269	1.00[ASN][1000 genomes]
rs6722440	0.87[EUR][1000 genomes]
rs6729569	0.87[CEU][hapmap]
rs6729604	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6743966	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6755303	0.88[CEU][hapmap]
rs6758093	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6758512	0.87[EUR][1000 genomes]
rs7560422	1.00[ASN][1000 genomes]
rs7565420	0.87[EUR][1000 genomes]
rs7586004	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7595101	1.00[ASN][1000 genomes]
rs9973504	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13423962	MCFD2	cis	multi-tissue	Pritchard
rs13423962	MMP20	trans	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169600-47183600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:47169800-47182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:47169800-47182200	Weak transcription	Right Ventricle	heart
4	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
5	chr2:47170000-47181600	Weak transcription	HUVEC	blood vessel
6	chr2:47170000-47182200	Weak transcription	Psoas Muscle	Psoas
7	chr2:47170200-47181400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:47170800-47184000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:47171000-47182600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:47171200-47182400	Weak transcription	Small Intestine	intestine
11	chr2:47171400-47182000	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:47171800-47181400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:47171800-47181400	Weak transcription	Right Atrium	heart
14	chr2:47173000-47191800	Weak transcription	Fetal Brain Male	brain
15	chr2:47173400-47181600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:47173400-47184000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:47174000-47182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:47174200-47183800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:47174200-47184200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:47174800-47181400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:47175600-47181600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:47176200-47181200	Strong transcription	Fetal Intestine Small	intestine
24	chr2:47176400-47192600	Strong transcription	Dnd41	blood
25	chr2:47177200-47181200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:47177200-47181800	Genic enhancers	A549	lung
27	chr2:47177200-47185000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:47177400-47180800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr2:47177400-47180800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr2:47177400-47181000	Strong transcription	Brain Angular Gyrus	brain
32	chr2:47177400-47182000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:47177400-47192800	Strong transcription	Fetal Stomach	stomach
34	chr2:47177600-47181000	Strong transcription	NHEK	skin
35	chr2:47177600-47181200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:47177600-47181200	Strong transcription	Osteobl	bone
37	chr2:47177600-47181400	Strong transcription	Stomach Smooth Muscle	stomach
38	chr2:47177600-47181400	Strong transcription	NHLF	lung
39	chr2:47177600-47181600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:47177600-47181600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:47177600-47181600	Strong transcription	Placenta	Placenta
42	chr2:47177600-47181800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:47177600-47181800	Strong transcription	Esophagus	oesophagus
44	chr2:47177600-47182000	Strong transcription	Brain Hippocampus Middle	brain
45	chr2:47177600-47182000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr2:47177600-47182000	Strong transcription	Brain Substantia Nigra	brain
47	chr2:47177600-47182800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr2:47177600-47183200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:47177600-47188200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:47177600-47190000	Strong transcription	Primary T cells fromperipheralblood	blood

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