Variant report

Variant	rs2140913
Chromosome Location	chr7:112728053-112728054
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	chr7:112726439-112728146	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr7:112727370-112728176	SK-N-MC	brain:	n/a	n/a
3	IRF1	chr7:112726174-112728305	K562	blood:	n/a	chr7:112727424-112727438 chr7:112727424-112727437
4	ATF1	chr7:112727241-112728091	K562	blood:	n/a	n/a
5	PML	chr7:112727100-112728186	K562	blood:	n/a	n/a
6	JUND	chr7:112727352-112728274	K562	blood:	n/a	chr7:112728177-112728186 chr7:112727855-112727864
7	EP300	chr7:112727369-112728272	K562	blood:	n/a	n/a
8	CCNT2	chr7:112727754-112728281	K562	blood:	n/a	chr7:112727922-112727942
9	RFX5	chr7:112727673-112728076	K562	blood:	n/a	chr7:112727854-112727863
10	GATA3	chr7:112727054-112728298	SK-N-SH	brain:	n/a	chr7:112727923-112727931 chr7:112727924-112727931 chr7:112727925-112727942 chr7:112727921-112727931
11	CEBPD	chr7:112727558-112728128	K562	blood:	n/a	n/a
12	MAX	chr7:112727220-112728380	SK-N-SH	brain:	n/a	n/a
13	MYC	chr7:112726580-112728261	K562	blood:	n/a	chr7:112726902-112726912 chr7:112726898-112726908
14	REST	chr7:112723245-112728173	H1-neurons	neurons:	n/a	chr7:112726833-112726847 chr7:112726902-112726915
15	GATA3	chr7:112727563-112728705	SH-SY5Y	brain:	n/a	chr7:112727923-112727931 chr7:112727924-112727931 chr7:112727925-112727942 chr7:112727921-112727931
16	POLR2A	chr7:112727068-112728056	H1-neurons	neurons:	n/a	n/a
17	MXI1	chr7:112725259-112728607	SK-N-SH	brain:	n/a	n/a
18	FOS	chr7:112727701-112728104	K562	blood:	n/a	chr7:112727855-112727864
19	CEBPB	chr7:112727365-112728255	K562	blood:	n/a	n/a
20	TAL1	chr7:112727329-112728122	K562	blood:	n/a	chr7:112727924-112727942
21	ARID3A	chr7:112727223-112728259	K562	blood:	n/a	n/a
22	POLR2A	chr7:112727120-112728171	H1-neurons	neurons:	n/a	n/a
23	JUN	chr7:112727413-112728153	K562	blood:	n/a	chr7:112727855-112727864
24	CEBPB	chr7:112727317-112728105	IMR90	lung:	n/a	n/a
25	MYC	chr7:112726665-112728276	K562	blood:	n/a	chr7:112726902-112726912 chr7:112726898-112726908
26	GATA2	chr7:112727315-112728107	SH-SY5Y	brain:	n/a	chr7:112727924-112727931 chr7:112727925-112727942 chr7:112727921-112727931
27	CEBPB	chr7:112727379-112728119	K562	blood:	n/a	n/a
28	CEBPD	chr7:112727157-112728155	K562	blood:	n/a	n/a
29	POLR2A	chr7:112727067-112728098	U87	brain:	n/a	n/a
30	TEAD4	chr7:112727282-112728124	K562	blood:	n/a	n/a
31	RCOR1	chr7:112725762-112728325	K562	blood:	n/a	n/a
32	NFYB	chr7:112727692-112728061	K562	blood:	n/a	chr7:112727851-112727865
33	NFYA	chr7:112727234-112728413	K562	blood:	n/a	chr7:112727851-112727869 chr7:112727851-112727865 chr7:112728389-112728401 chr7:112728388-112728398
34	POLR2A	chr7:112727067-112728092	U87	brain:	n/a	n/a
35	GATA3	chr7:112727074-112728519	SK-N-SH	brain:	n/a	chr7:112727923-112727931 chr7:112727924-112727931 chr7:112727925-112727942 chr7:112727921-112727931
36	TEAD4	chr7:112725724-112728342	K562	blood:	n/a	chr7:112728159-112728168
37	MAX	chr7:112727244-112728260	NB4	blood:	n/a	n/a
38	GATA1	chr7:112727651-112728299	PBDE	blood:	n/a	chr7:112727924-112727931 chr7:112727925-112727942 chr7:112727921-112727931
39	TBP	chr7:112726014-112728059	K562	blood:	n/a	n/a
40	RFX5	chr7:112724778-112728809	SK-N-SH	brain:	n/a	chr7:112727854-112727863
41	NRF1	chr7:112725709-112728173	SK-N-SH	brain:	n/a	chr7:112726541-112726550 chr7:112726539-112726550 chr7:112726539-112726550 chr7:112726539-112726553 chr7:112726536-112726550
42	PBX3	chr7:112727036-112728560	SK-N-SH	brain:	n/a	chr7:112727854-112727863 chr7:112728101-112728112
43	MYC	chr7:112726596-112728195	NB4	blood:	n/a	chr7:112726902-112726912 chr7:112726898-112726908

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112723161..112726364-chr7:112726656..112729737,3	K562	blood:
2	chr7:112725765..112728466-chr7:112738917..112741049,2	K562	blood:

Variant related genes	Relation type
GPR85	TF binding region
ENSG00000225457	Chromatin interaction
ENSG00000164604	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1008056	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1013638	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10225200	1.00[JPT][hapmap]
rs10228219	1.00[JPT][hapmap]
rs10228566	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10232392	1.00[JPT][hapmap]
rs10232914	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10241250	1.00[JPT][hapmap]
rs10241676	1.00[JPT][hapmap]
rs10241909	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10245805	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10246011	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10246012	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10249359	1.00[JPT][hapmap]
rs10252483	1.00[JPT][hapmap]
rs10257270	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10258099	1.00[JPT][hapmap]
rs10261482	1.00[JPT][hapmap]
rs10261563	1.00[JPT][hapmap]
rs10267369	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10267575	1.00[JPT][hapmap]
rs10267803	1.00[JPT][hapmap]
rs10269536	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10270797	1.00[JPT][hapmap]
rs10278104	1.00[JPT][hapmap]
rs10278248	1.00[JPT][hapmap]
rs10278935	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10280900	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500019	1.00[JPT][hapmap]
rs1051997	0.85[CEU][hapmap]
rs12386568	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670138	1.00[JPT][hapmap]
rs12672405	1.00[JPT][hapmap]
rs12672763	1.00[JPT][hapmap]
rs1575013	0.80[CEU][hapmap];0.97[ASN][1000 genomes]
rs1590155	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1599792	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599793	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599794	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17160251	1.00[JPT][hapmap]
rs17160260	1.00[JPT][hapmap]
rs1807909	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2037657	0.85[CEU][hapmap]
rs2177800	0.85[CEU][hapmap];0.83[CHD][hapmap]
rs2245834	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245985	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2246845	1.00[JPT][hapmap]
rs2249253	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2249501	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2249511	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2249612	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2250343	0.85[CEU][hapmap]
rs2253773	0.85[CEU][hapmap]
rs2254842	0.85[CEU][hapmap]
rs2264731	0.94[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2264732	0.84[CEU][hapmap]
rs2272261	1.00[JPT][hapmap]
rs2462665	0.85[CEU][hapmap]
rs28658090	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55822923	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55836916	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56182321	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56202345	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56311133	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56408134	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73198873	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73198882	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7787425	1.00[JPT][hapmap]
rs872944	1.00[JPT][hapmap]
rs9656199	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9656200	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758131	chr7:112492127-112768628	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759556	chr7:112492127-112768628	Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3355135	chr7:112616979-113134651	Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv435847	chr7:112618576-113134022	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3430638	chr7:112620663-113134403	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3442221	chr7:112620665-113134971	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv993501	chr7:112625029-113125338	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1022066	chr7:112630168-113122748	Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv539090	chr7:112630168-113122748	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv889057	chr7:112652854-112734225	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
11	nsv889058	chr7:112652854-112737222	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2140913	GPR85	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112725600-112728200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:112725600-112728200	Active TSS	Aorta	Aorta
3	chr7:112726400-112728200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr7:112726400-112728200	Active TSS	NH-A	brain
5	chr7:112726800-112739200	Weak transcription	Fetal Heart	heart
6	chr7:112727200-112728200	Flanking Active TSS	K562	blood
7	chr7:112727600-112728200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
8	chr7:112727600-112728200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr7:112727800-112728200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr7:112727800-112728200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr7:112727800-112728200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr7:112727800-112728200	Enhancers	Fetal Stomach	stomach
13	chr7:112727800-112728800	Enhancers	HSMM	muscle
14	chr7:112728000-112728200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr7:112728000-112728200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr7:112728000-112728200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:112728000-112728200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr7:112728000-112728200	Flanking Active TSS	Fetal Brain Male	brain
19	chr7:112728000-112728200	Enhancers	NHDF-Ad	bronchial
20	chr7:112728000-112728200	Flanking Active TSS	Osteobl	bone
21	chr7:112728000-112728400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr7:112728000-112728400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:112728000-112728600	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links