Variant report

Variant	rs1900921
Chromosome Location	chr15:42787144-42787145
allele	A/C
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	POLR2A	chr15:42787126-42788645	K562	blood:	n/a	n/a
2	POLR2A	chr15:42787099-42788295	MCF10A-Er-Src	breast:	n/a	n/a
3	MAX	chr15:42787131-42788247	SK-N-SH	brain:	n/a	chr15:42788027-42788037
4	GABPA	chr15:42787099-42787981	SK-N-SH	brain:	n/a	chr15:42787827-42787841 chr15:42787804-42787818 chr15:42787827-42787836 chr15:42787824-42787838 chr15:42787827-42787838
5	RCOR1	chr15:42787131-42788446	K562	blood:	n/a	n/a
6	POLR2A	chr15:42787131-42787160	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:42787068-42788146	U87	brain:	n/a	n/a
8	POLR2A	chr15:42787010-42788624	IMR90	lung:	n/a	n/a
9	MXI1	chr15:42787031-42788435	IMR90	lung:	n/a	n/a
10	POLR2A	chr15:42787128-42788354	Hela-S3	cervix:	n/a	n/a
11	NR2F2	chr15:42787066-42788568	K562	blood:	n/a	n/a
12	POLR2A	chr15:42787014-42788172	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr15:42787043-42788218	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr15:42787009-42788258	U87	brain:	n/a	n/a
15	GABPA	chr15:42787138-42787519	MCF-7	breast:	n/a	n/a
16	POLR2A	chr15:42786933-42788805	HUVEC	blood vessel:	n/a	n/a
17	GATA1	chr15:42787093-42788685	PBDE	blood:	n/a	n/a
18	HEY1	chr15:42787097-42788196	HepG2	liver:	n/a	chr15:42787819-42787834
19	GABPA	chr15:42787112-42787854	A549	lung:	n/a	chr15:42787827-42787841 chr15:42787804-42787818 chr15:42787827-42787836 chr15:42787824-42787838 chr15:42787827-42787838
20	TAF1	chr15:42787096-42787479	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr15:42787003-42788264	U87	brain:	n/a	n/a
22	POLR2A	chr15:42787104-42788133	ProgFib	skin:	n/a	n/a
23	MXI1	chr15:42787013-42788664	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr15:42787089-42788359	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr15:42787123-42788148	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr15:42787115-42788406	GM12891	blood:	n/a	n/a
27	POLR2A	chr15:42787071-42788275	HepG2	liver:	n/a	n/a
28	ELK4	chr15:42787097-42788063	Hela-S3	cervix:	n/a	chr15:42787351-42787362
29	POLR2A	chr15:42787102-42788266	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr15:42787089-42788363	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr15:42787089-42788172	U87	brain:	n/a	n/a
32	POLR2A	chr15:42787090-42788371	Hela-S3	cervix:	n/a	n/a
33	GABPA	chr15:42787143-42787959	Hela-S3	cervix:	n/a	chr15:42787827-42787841 chr15:42787804-42787818 chr15:42787827-42787836 chr15:42787824-42787838 chr15:42787827-42787838
34	PML	chr15:42787130-42788552	K562	blood:	n/a	n/a
35	GABPA	chr15:42786975-42788016	MCF-7	breast:	n/a	chr15:42787827-42787841 chr15:42787804-42787818 chr15:42787827-42787836 chr15:42787824-42787838 chr15:42787827-42787838
36	POLR2A	chr15:42787116-42788363	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr15:42786899-42788744	HUVEC	blood vessel:	n/a	n/a
38	MAX	chr15:42787043-42788364	SK-N-SH	brain:	n/a	chr15:42788027-42788037
39	POLR2A	chr15:42787144-42788523	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42781216..42785618-chr15:42786050..42793334,15	K562	blood:
2	chr15:42786881..42789392-chr15:42840485..42842780,2	K562	blood:
3	chr15:42785710..42787693-chr15:42866156..42868186,2	K562	blood:
4	chr15:42781833..42785082-chr15:42786422..42789177,6	MCF-7	breast:
5	chr15:42781216..42785097-chr15:42786050..42789793,8	K562	blood:

Variant related genes	Relation type
ZNF106	TF binding region
SNAP23	TF binding region
ENSG00000092531	Chromatin interaction
ENSG00000137814	Chromatin interaction
ENSG00000103994	Chromatin interaction
ENSG00000159433	Chromatin interaction
ENSG00000180979	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10454039	0.90[EUR][1000 genomes]
rs10518763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10518766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1060291	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060293	1.00[ASN][1000 genomes]
rs10851410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10851411	0.86[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs11022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070374	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs11070376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11631193	0.88[EUR][1000 genomes]
rs11636577	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638208	0.86[EUR][1000 genomes]
rs12324113	0.93[EUR][1000 genomes]
rs12324717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12903432	0.95[EUR][1000 genomes]
rs12906697	0.90[EUR][1000 genomes]
rs12913324	0.82[EUR][1000 genomes]
rs16973053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973054	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973089	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973091	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973093	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973095	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973097	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973107	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973132	1.00[CHB][hapmap]
rs16973137	1.00[CHB][hapmap]
rs16973148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973155	1.00[CHB][hapmap]
rs16973171	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17695121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17709180	1.00[ASN][1000 genomes]
rs17709377	1.00[ASN][1000 genomes]
rs17766532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2241998	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs2255995	0.95[EUR][1000 genomes]
rs2412704	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2595939	0.95[EUR][1000 genomes]
rs2595940	0.95[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs2595941	0.94[EUR][1000 genomes]
rs2617236	0.95[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs28364347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28886308	0.84[EUR][1000 genomes]
rs2899051	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899057	0.89[EUR][1000 genomes]
rs2899059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34359922	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34643746	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34792942	1.00[ASN][1000 genomes]
rs3986280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344713	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4573906	0.95[EUR][1000 genomes]
rs4923948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924684	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924687	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56357092	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56982416	1.00[ASN][1000 genomes]
rs58042601	1.00[ASN][1000 genomes]
rs58641431	1.00[ASN][1000 genomes]
rs59697584	1.00[ASN][1000 genomes]
rs59705032	1.00[ASN][1000 genomes]
rs60380503	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60584955	1.00[ASN][1000 genomes]
rs60812675	1.00[ASN][1000 genomes]
rs61489160	1.00[ASN][1000 genomes]
rs62022317	1.00[ASN][1000 genomes]
rs7164437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7164874	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7165023	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7178901	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7180483	1.00[ASN][1000 genomes]
rs7182797	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73402783	1.00[ASN][1000 genomes]
rs73402785	1.00[ASN][1000 genomes]
rs73404714	1.00[ASN][1000 genomes]
rs73404723	1.00[ASN][1000 genomes]
rs73404730	1.00[ASN][1000 genomes]
rs73404763	1.00[ASN][1000 genomes]
rs73406518	1.00[ASN][1000 genomes]
rs73406534	1.00[ASN][1000 genomes]
rs73406545	1.00[ASN][1000 genomes]
rs74009095	1.00[ASN][1000 genomes]
rs8033412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9302112	0.95[CEU][hapmap];0.88[TSI][hapmap];0.95[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	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1900921	TMCO5A	cis	parietal	SCAN
rs1900921	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs1900921	INO80	cis	parietal	SCAN
rs1900921	SNAP23	cis	parietal	SCAN
rs1900921	CXorf57	trans	parietal	SCAN
rs1900921	MAP1A	cis	parietal	SCAN
rs1900921	TNPO2	trans	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42783400-42787400	Weak transcription	Gastric	stomach
2	chr15:42783600-42787200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:42783600-42787400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:42783600-42787800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:42783600-42787800	Weak transcription	Spleen	Spleen
6	chr15:42783800-42787200	Enhancers	Placenta	Placenta
7	chr15:42783800-42787400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:42783800-42787400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:42784000-42787200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:42784000-42787200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:42784000-42787200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:42784000-42787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:42784000-42787200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:42784000-42787200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:42784000-42787200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:42784200-42787200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:42784200-42787200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:42784200-42787400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:42784400-42787200	Weak transcription	Right Atrium	heart
20	chr15:42785000-42787800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr15:42785000-42789000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr15:42786200-42787200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:42786800-42787200	Enhancers	Esophagus	oesophagus
24	chr15:42786800-42787200	Enhancers	Lung	lung
25	chr15:42786800-42787200	Enhancers	Pancreas	Pancrea
26	chr15:42786800-42787200	Enhancers	GM12878-XiMat	blood
27	chr15:42786800-42787400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr15:42786800-42787400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr15:42786800-42789200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:42787000-42787200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:42787000-42787200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:42787000-42787200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:42787000-42787200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:42787000-42787200	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr15:42787000-42787200	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr15:42787000-42787200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:42787000-42787200	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr15:42787000-42787200	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr15:42787000-42787200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr15:42787000-42787200	Enhancers	Fetal Heart	heart
41	chr15:42787000-42787200	Enhancers	Fetal Intestine Large	intestine
42	chr15:42787000-42787200	Enhancers	Fetal Intestine Small	intestine
43	chr15:42787000-42787200	Enhancers	Fetal Kidney	kidney
44	chr15:42787000-42787200	Enhancers	Fetal Stomach	stomach
45	chr15:42787000-42787200	Enhancers	Fetal Thymus	thymus
46	chr15:42787000-42787200	Enhancers	Small Intestine	intestine
47	chr15:42787000-42787200	Weak transcription	Stomach Mucosa	stomach
48	chr15:42787000-42787200	Flanking Active TSS	HSMM	muscle
49	chr15:42787000-42787200	Flanking Active TSS	NHDF-Ad	bronchial
50	chr15:42787000-42787200	Enhancers	NHLF	lung

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