Variant report

Variant	rs12698896
Chromosome Location	chr7:69779149-69779150
allele	C/T
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	REST	chr7:69778346-69779782	H1-neurons	neurons:	n/a	chr7:69778929-69778949
2	POLR2A	chr7:69779132-69779615	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr7:69779003-69779613	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
AUTS2	TF binding region

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10229027	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10229155	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10234614	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10234844	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10234892	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10235487	0.81[ASN][1000 genomes]
rs10235781	0.84[ASN][1000 genomes]
rs10237530	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10237685	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10244275	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10246631	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10251416	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10254839	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10256062	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10258298	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10258962	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10268924	0.85[ASN][1000 genomes]
rs10277411	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10280622	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1035010	0.81[ASN][1000 genomes]
rs10486874	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10486875	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10950199	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11766329	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12112638	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12155138	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374873	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698855	0.81[ASN][1000 genomes]
rs12698871	0.85[ASN][1000 genomes]
rs12698895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698897	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698899	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13221252	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226923	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13228123	0.81[ASN][1000 genomes]
rs1357759	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1404274	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1464786	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1464787	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1464788	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474368	0.90[ASN][1000 genomes]
rs1524518	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880368	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103132	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2222544	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2280613	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280614	0.87[EUR][1000 genomes]
rs2866277	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35303761	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3846984	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460536	0.81[ASN][1000 genomes]
rs6460537	0.85[ASN][1000 genomes]
rs6460541	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6460542	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460543	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651055	0.85[ASN][1000 genomes]
rs6943555	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6950647	0.85[ASN][1000 genomes]
rs6953344	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6954715	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954837	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957740	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6961345	0.85[ASN][1000 genomes]
rs6962999	0.81[ASN][1000 genomes]
rs6967697	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6967986	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6969375	0.87[EUR][1000 genomes]
rs6975279	0.85[ASN][1000 genomes]
rs6976581	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7781401	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7781727	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7784584	0.83[ASN][1000 genomes]
rs7787612	0.91[EUR][1000 genomes]
rs7790729	0.85[ASN][1000 genomes]
rs7792775	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792964	0.90[EUR][1000 genomes]
rs7796080	0.85[ASN][1000 genomes]
rs7798991	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7799308	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7805470	0.86[ASN][1000 genomes]
rs8180850	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs870920	0.86[ASN][1000 genomes]
rs873835	0.86[ASN][1000 genomes]
rs9918496	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9918544	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv532782	chr7:69383651-70189959	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv916345	chr7:69520612-69784809	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv869342	chr7:69671501-69958576	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv607431	chr7:69699074-69828729	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv888337	chr7:69707076-69952187	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv529669	chr7:69709373-69974708	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1028870	chr7:69742438-69879231	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69776000-69786600	Enhancers	Primary T cells from cord blood	blood
2	chr7:69776600-69782000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:69777600-69779200	Enhancers	H1 Cell Line	embryonic stem cell
4	chr7:69777800-69781600	Weak transcription	Dnd41	blood
5	chr7:69778000-69779200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr7:69778000-69779400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr7:69778000-69780800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:69778000-69781800	Weak transcription	Fetal Thymus	thymus
9	chr7:69778200-69779200	Enhancers	Fetal Kidney	kidney
10	chr7:69778200-69779400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:69778200-69779400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:69778200-69782000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:69778200-69782600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr7:69778400-69780600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:69778400-69781600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:69778600-69789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:69778800-69779200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr7:69778800-69779200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:69778800-69781200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr7:69778800-69782800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr7:69779000-69779400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:69779000-69779600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:69779000-69781600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:69779000-69783400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:69779000-69783600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr7:69779000-69784000	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links