Variant report

Variant	rs7931681
Chromosome Location	chr11:108004798-108004799
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	STAT3	chr11:108004766-108004874	MCF10A-Er-Src	breast:	n/a	chr11:108004842-108004853 chr11:108004861-108004869
2	POLR2A	chr11:108004043-108005001	K562	blood:	n/a	n/a
3	CEBPB	chr11:108004752-108005005	HepG2	liver:	n/a	chr11:108004860-108004869
4	CEBPB	chr11:108004786-108004880	A549	lung:	n/a	chr11:108004860-108004869

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:108004225..108006162-chr11:108007961..108009526,2	K562	blood:

Variant related genes	Relation type
ACAT1	TF binding region
ENSG00000075239	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1003624	0.81[CHB][hapmap]
rs10890817	0.90[YRI][hapmap]
rs11212484	0.87[CEU][hapmap]
rs11212524	0.95[YRI][hapmap]
rs11212525	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11212551	0.86[JPT][hapmap]
rs11605442	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs12360727	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12786416	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12787445	0.81[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs12794010	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1519073	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1550609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1607476	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs183459	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs183460	0.86[JPT][hapmap]
rs1850730	0.86[JPT][hapmap]
rs2056267	0.84[JPT][hapmap]
rs2070661	0.86[JPT][hapmap]
rs2083707	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs228589	0.86[JPT][hapmap]
rs34971817	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736509	0.83[CEU][hapmap]
rs3781868	0.90[JPT][hapmap]
rs4028262	0.87[CEU][hapmap]
rs4623864	0.86[JPT][hapmap]
rs4754299	0.80[ASN][1000 genomes]
rs4754305	0.86[JPT][hapmap]
rs4987982	0.82[CHB][hapmap]
rs609557	0.86[JPT][hapmap]
rs618499	0.82[CHB][hapmap]
rs6589007	0.86[JPT][hapmap]
rs664677	0.82[CHB][hapmap]
rs7118967	0.80[CHB][hapmap];0.86[JPT][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	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv3372573	chr11:107880365-108022895	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1039549	chr11:107950572-108034548	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1040522	chr11:107969357-108049672	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7931681	NPAT	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107993200-108013200	Weak transcription	Fetal Thymus	thymus
2	chr11:107993200-108018600	Weak transcription	Thymus	Thymus
3	chr11:107993200-108021800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:107993200-108030000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:107993200-108069600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:107993400-108006000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:107993400-108009600	Weak transcription	Colonic Mucosa	Colon
8	chr11:107993400-108011200	Weak transcription	Esophagus	oesophagus
9	chr11:107993400-108012600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:107993400-108013200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:107993400-108014000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:107993400-108017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:107993600-108005800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:107993600-108005800	Weak transcription	NH-A	brain
15	chr11:107993600-108006600	Weak transcription	HMEC	breast
16	chr11:107993600-108006800	Weak transcription	HSMMtube	muscle
17	chr11:107993600-108013200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:107993600-108018800	Weak transcription	Fetal Kidney	kidney
19	chr11:107993800-108010800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:107994000-108029600	Weak transcription	Fetal Brain Male	brain
21	chr11:107994200-108005800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:107994600-108009400	Weak transcription	Fetal Brain Female	brain
23	chr11:107994600-108013800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:107994800-108009400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr11:107994800-108011600	Weak transcription	Fetal Intestine Small	intestine
26	chr11:107995000-108005800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:107995000-108005800	Weak transcription	NHLF	lung
28	chr11:107995000-108018600	Weak transcription	Hela-S3	cervix
29	chr11:107995200-108010800	Weak transcription	Brain Germinal Matrix	brain
30	chr11:107995200-108011200	Weak transcription	Primary B cells from cord blood	blood
31	chr11:107995200-108011400	Weak transcription	Aorta	Aorta
32	chr11:107995400-108005800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:107995400-108011200	Weak transcription	Lung	lung
34	chr11:107995400-108011200	Weak transcription	Spleen	Spleen
35	chr11:107995400-108011600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:107995400-108013000	Weak transcription	Dnd41	blood
37	chr11:107995400-108013200	Weak transcription	Gastric	stomach
38	chr11:107995600-108006000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:107995600-108009400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:107995600-108011800	Weak transcription	Small Intestine	intestine
41	chr11:107995600-108017800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr11:107995800-108005800	Weak transcription	HepG2	liver
43	chr11:107995800-108011200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:107995800-108011400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr11:107995800-108013000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr11:107996000-108006600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:107996000-108021400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr11:107996200-108005800	Weak transcription	A549	lung
49	chr11:107996200-108005800	Weak transcription	K562	blood
50	chr11:107996200-108019200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links