Variant report

Variant	rs17723260
Chromosome Location	chr1:155058663-155058664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:33)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:33 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154970467..154977420-chr1:155052491..155060843,19	MCF-7	breast:
2	chr1:155056804..155058815-chr1:155240733..155243389,2	K562	blood:
3	chr1:155017547..155018103-chr1:155058250..155059160,2	K562	blood:
4	chr1:155054721..155059011-chr1:155196588..155199418,3	K562	blood:
5	chr1:154964452..154967253-chr1:155056119..155059048,2	MCF-7	breast:
6	chr1:155056523..155059485-chr1:155177407..155180672,3	K562	blood:
7	chr1:155055553..155060043-chr1:155139937..155145817,8	K562	blood:
8	chr1:155056284..155060443-chr1:155143066..155147437,8	MCF-7	breast:
9	chr1:155057862..155060802-chr1:155145958..155147519,2	K562	blood:
10	chr1:154938611..154941490-chr1:155057349..155058983,2	MCF-7	breast:
11	chr1:154967268..154977621-chr1:155049775..155059069,28	MCF-7	breast:
12	chr1:154949477..154951157-chr1:155056165..155059082,2	K562	blood:
13	chr1:155056491..155066482-chr1:155136760..155147519,21	K562	blood:
14	chr1:154529703..154532693-chr1:155057067..155059987,2	K562	blood:
15	chr1:155055823..155058786-chr1:155242892..155244549,2	MCF-7	breast:
16	chr1:155034804..155037518-chr1:155055135..155058799,58	K562	blood:
17	chr1:155058320..155058876-chr1:155140102..155140961,2	MCF-7	breast:
18	chr1:155058008..155061537-chr1:155106258..155110440,4	K562	blood:
19	chr1:154908623..154911481-chr1:155056952..155059272,2	MCF-7	breast:
20	chr1:155056751..155059603-chr1:155143653..155146036,8	MCF-7	breast:
21	chr1:154933652..154935727-chr1:155055132..155058797,5	MCF-7	breast:
22	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
23	chr1:154931665..154935409-chr1:155055892..155060477,8	MCF-7	breast:
24	chr1:155013927..155032770-chr1:155044175..155061131,53	MCF-7	breast:
25	chr1:155057155..155059036-chr1:155292671..155295446,3	MCF-7	breast:
26	chr1:155052471..155058946-chr1:155106509..155113930,10	K562	blood:
27	chr1:155020796..155024695-chr1:155055166..155059924,7	K562	blood:
28	chr1:155052798..155059451-chr1:155162483..155166744,9	K562	blood:
29	chr1:154878924..154879433-chr1:155058429..155059146,2	MCF-7	breast:
30	chr1:155058160..155059043-chr6:31795196..31795706,2	Hela-S3	cervix:
31	chr1:155057429..155059186-chr1:155111199..155113045,2	K562	blood:
32	chr1:154941529..154944421-chr1:155058402..155060354,2	K562	blood:
33	chr1:155056530..155058756-chr1:155164406..155166791,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169242	Chromatin interaction
ENSG00000270361	Chromatin interaction
ENSG00000271380	Chromatin interaction
ENSG00000202027	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000160688	Chromatin interaction
ENSG00000173171	Chromatin interaction
ENSG00000160753	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000232093	Chromatin interaction
ENSG00000231064	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000225855	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000173207	Chromatin interaction
ENSG00000204388	Chromatin interaction
ENSG00000160714	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000163352	Chromatin interaction
ENSG00000176444	Chromatin interaction
ENSG00000163344	Chromatin interaction
ENSG00000163348	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11264305	1.00[ASN][1000 genomes]
rs12743272	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34522020	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765087	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4845407	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4971092	1.00[CHD][hapmap];0.87[GIH][hapmap]
rs6427184	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17723260	EFNA1	cis	cerebellum	SCAN
rs17723260	APOA1BP	cis	cerebellum	SCAN
rs17723260	S100A3	cis	parietal	SCAN
rs17723260	RPRD2	cis	parietal	SCAN
rs17723260	C1orf54	cis	cerebellum	SCAN
rs17723260	TPM3	cis	parietal	SCAN
rs17723260	SMCP	cis	cerebellum	SCAN
rs17723260	RXFP4	cis	parietal	SCAN
rs17723260	TDRKH	cis	cerebellum	SCAN
rs17723260	C1orf56	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155057000-155058800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr1:155057000-155058800	Active TSS	A549	lung
3	chr1:155057200-155058800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:155057200-155058800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr1:155057200-155058800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:155057200-155058800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:155057200-155058800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:155057200-155058800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:155057200-155058800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:155057200-155058800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:155057200-155058800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:155057200-155058800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr1:155057200-155059000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:155057800-155058800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:155058000-155058800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr1:155058000-155058800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr1:155058000-155058800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:155058000-155058800	Flanking Active TSS	Fetal Intestine Small	intestine
19	chr1:155058000-155058800	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr1:155058000-155058800	Flanking Active TSS	HMEC	breast
21	chr1:155058000-155059000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:155058000-155059000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:155058000-155059000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr1:155058000-155059000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr1:155058000-155059000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:155058000-155059000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:155058000-155059000	Flanking Active TSS	K562	blood
28	chr1:155058000-155059200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:155058000-155059200	Flanking Active TSS	Dnd41	blood
30	chr1:155058000-155059200	Flanking Active TSS	Hela-S3	cervix
31	chr1:155058000-155059400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:155058000-155059600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:155058200-155058800	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr1:155058200-155059000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:155058200-155059200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:155058200-155059200	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:155058200-155059800	Enhancers	Fetal Brain Male	brain
38	chr1:155058200-155060200	Enhancers	Fetal Heart	heart
39	chr1:155058400-155058800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:155058400-155059000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:155058400-155059000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:155058400-155059000	Enhancers	Primary T cells from cord blood	blood
43	chr1:155058400-155059000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr1:155058400-155059000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:155058400-155059000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr1:155058400-155059000	Enhancers	Brain Cingulate Gyrus	brain
47	chr1:155058400-155059000	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr1:155058400-155059000	Enhancers	Fetal Brain Female	brain
49	chr1:155058400-155059000	Enhancers	Fetal Stomach	stomach
50	chr1:155058400-155059000	Enhancers	Gastric	stomach

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