Variant report

Variant	rs11638130
Chromosome Location	chr15:75183935-75183936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr15:75183414-75184018	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr15:75183538-75184396	SK-N-MC	brain:	n/a	n/a
3	HNF4G	chr15:75183701-75184075	HepG2	liver:	n/a	chr15:75183936-75183949 chr15:75183936-75183949 chr15:75183934-75183952 chr15:75183932-75183954 chr15:75183936-75183949 chr15:75183937-75183950 chr15:75183937-75183949
4	HNF4A	chr15:75183745-75184089	HepG2	liver:	n/a	chr15:75183936-75183949 chr15:75183936-75183949 chr15:75183934-75183952 chr15:75183932-75183954 chr15:75183936-75183949 chr15:75183937-75183950 chr15:75183937-75183949 chr15:75183935-75183950
5	POLR2A	chr15:75183893-75184114	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr15:75183928-75184167	K562	blood:	n/a	n/a
7	POLR2A	chr15:75183524-75184101	HepG2	liver:	n/a	n/a
8	HNF4A	chr15:75183700-75184055	HepG2	liver:	n/a	chr15:75183936-75183949 chr15:75183936-75183949 chr15:75183934-75183952 chr15:75183932-75183954 chr15:75183936-75183949 chr15:75183937-75183950 chr15:75183937-75183949 chr15:75183935-75183950
9	POLR2A	chr15:75183559-75184234	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr15:75183511-75184317	K562	blood:	n/a	n/a
11	POLR2A	chr15:75183870-75184178	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75163351..75167012-chr15:75180238..75185061,13	MCF-7	breast:
2	chr15:75167898..75170533-chr15:75183102..75184983,2	K562	blood:
3	chr15:75156545..75159476-chr15:75183223..75185437,3	MCF-7	breast:
4	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
5	chr15:75072788..75075776-chr15:75181274..75184204,2	K562	blood:
6	chr15:75127539..75130871-chr15:75182053..75185205,4	MCF-7	breast:
7	chr15:75080217..75082228-chr15:75182575..75184955,2	MCF-7	breast:
8	chr15:75081397..75085815-chr15:75182279..75185381,4	MCF-7	breast:
9	chr15:75072512..75079183-chr15:75180576..75186728,11	MCF-7	breast:
10	chr15:75162469..75167536-chr15:75180880..75184902,6	K562	blood:
11	chr15:75181107..75185393-chr15:75190667..75200295,16	MCF-7	breast:
12	chr15:75163342..75166719-chr15:75180364..75184673,7	MCF-7	breast:
13	chr15:75182085..75184679-chr15:75247604..75250598,2	MCF-7	breast:
14	chr15:75116359..75118172-chr15:75182130..75184765,2	MCF-7	breast:
15	chr15:75133683..75136875-chr15:75181140..75184004,7	K562	blood:
16	chr15:75163901..75170368-chr15:75180139..75184021,10	K562	blood:
17	chr15:75072788..75075776-chr15:75181274..75184204,3	K562	blood:
18	chr15:75181707..75184142-chr2:24161514..24164019,2	MCF-7	breast:
19	chr15:75133950..75137156-chr15:75180779..75184661,9	MCF-7	breast:
20	chr15:75105024..75106901-chr15:75183732..75185502,2	MCF-7	breast:
21	chr15:75181382..75185367-chr15:75245501..75252189,8	K562	blood:

Variant related genes	Relation type
MPI	TF binding region
ENSG00000198794	Chromatin interaction
ENSG00000173960	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000264386	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000260824	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11072511	0.96[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs11072512	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072513	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072514	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1127796	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1130741	1.00[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs1133322	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1133323	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11630592	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11630918	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11633472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639413	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11854704	0.84[ASW][hapmap];0.96[CEU][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11856413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11857695	0.86[EUR][1000 genomes]
rs12487	0.84[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap]
rs12898539	0.80[AMR][1000 genomes]
rs12899787	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12900662	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12901190	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12902515	0.86[EUR][1000 genomes]
rs12903205	0.86[EUR][1000 genomes]
rs12903370	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12904326	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12904897	0.84[EUR][1000 genomes]
rs12907898	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12908365	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12909335	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12911254	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12912839	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12913293	0.89[EUR][1000 genomes]
rs12914217	0.83[AMR][1000 genomes]
rs1378942	1.00[LWK][hapmap]
rs2044157	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2168518	1.00[LWK][hapmap]
rs2290573	0.84[ASW][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap]
rs2415251	0.84[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35556055	0.91[MEX][hapmap]
rs3812945	0.83[MEX][hapmap]
rs4643278	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886608	0.84[EUR][1000 genomes]
rs4886632	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886636	0.96[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs4886639	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4886640	0.86[EUR][1000 genomes]
rs4886649	0.84[ASW][hapmap]
rs59945415	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62029167	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6495122	0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs7495664	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7495739	1.00[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs7497026	0.83[EUR][1000 genomes]
rs7497393	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8025447	0.88[EUR][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	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv990390	chr15:75179300-75187945	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11638130	SCAMP2	cis	Whole Blood	GTEx
rs11638130	TLE3	cis	cerebellum	SCAN
rs11638130	CSK	cis	lymphoblastoid	seeQTL
rs11638130	CYP1A1	cis	cerebellum	SCAN
rs11638130	ULK3	cis	parietal	SCAN
rs11638130	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs11638130	MPI	cis	lymphoblastoid	seeQTL
rs11638130	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs11638130	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs11638130	SCAMP2	cis	parietal	SCAN
rs11638130	SCAMP5	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75182200-75184000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:75182800-75184000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:75183000-75184000	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr15:75183000-75185400	Enhancers	Stomach Mucosa	stomach
5	chr15:75183200-75184000	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr15:75183200-75184000	Enhancers	Left Ventricle	heart
7	chr15:75183200-75184200	Enhancers	HSMMtube	muscle
8	chr15:75183200-75184600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:75183200-75184800	Weak transcription	Brain Germinal Matrix	brain
10	chr15:75183200-75184800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:75183200-75185000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:75183200-75185000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr15:75183200-75185000	Genic enhancers	Fetal Intestine Small	intestine
14	chr15:75183200-75185000	Enhancers	Right Atrium	heart
15	chr15:75183200-75185000	Enhancers	Right Ventricle	heart
16	chr15:75183200-75185000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr15:75183200-75185200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr15:75183200-75185200	Enhancers	Liver	Liver
19	chr15:75183200-75185200	Enhancers	Fetal Heart	heart
20	chr15:75183200-75185400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr15:75183200-75185800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:75183200-75186200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr15:75183200-75189400	Weak transcription	Psoas Muscle	Psoas
24	chr15:75183200-75191600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:75183200-75192000	Weak transcription	Fetal Kidney	kidney
26	chr15:75183200-75192400	Weak transcription	HUVEC	blood vessel
27	chr15:75183200-75197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr15:75183400-75184000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:75183400-75184200	Enhancers	Fetal Brain Male	brain
30	chr15:75183400-75184200	Enhancers	Small Intestine	intestine
31	chr15:75183400-75184600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:75183400-75184800	Weak transcription	Primary B cells from cord blood	blood
33	chr15:75183400-75184800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:75183400-75184800	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:75183400-75185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr15:75183400-75185000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:75183400-75185000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr15:75183400-75185200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:75183400-75185200	Genic enhancers	Fetal Intestine Large	intestine
40	chr15:75183400-75185200	Genic enhancers	Fetal Muscle Leg	muscle
41	chr15:75183400-75185200	Weak transcription	HSMM	muscle
42	chr15:75183400-75185400	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr15:75183400-75185600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr15:75183400-75185800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:75183400-75186000	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr15:75183400-75186200	Genic enhancers	Esophagus	oesophagus
47	chr15:75183400-75186200	Genic enhancers	Pancreas	Pancrea
48	chr15:75183400-75186200	Strong transcription	Osteobl	bone
49	chr15:75183400-75186400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:75183400-75186400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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