Variant report

Variant	rs1529641
Chromosome Location	chr11:8864138-8864139
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	CTCF	chr11:8864020-8864170	NHDF-neo	bronchial:	n/a	n/a
2	CTCF	chr11:8864040-8864190	AG04450	lung:	n/a	n/a
3	CTCF	chr11:8864060-8864210	BJ	skin:	n/a	n/a

Variant related genes	Relation type
RNA5SP330	TF binding region
ST5	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10743093	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10769947	0.82[CEU][hapmap]
rs10769948	0.82[CEU][hapmap]
rs10769957	0.82[CEU][hapmap]
rs10769967	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10769968	0.83[EUR][1000 genomes]
rs10769970	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10769971	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs10769973	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10769979	0.91[CEU][hapmap]
rs10840130	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs10840134	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10840135	0.82[JPT][hapmap]
rs10840136	0.84[ASN][1000 genomes]
rs10840141	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10840142	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10840147	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs10840148	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11042078	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs11042079	0.95[EUR][1000 genomes]
rs11042082	0.96[EUR][1000 genomes]
rs11042088	0.96[EUR][1000 genomes]
rs11042102	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11042103	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11042104	0.82[JPT][hapmap]
rs11042106	0.83[JPT][hapmap]
rs11042151	0.91[CEU][hapmap]
rs11042154	0.91[CEU][hapmap]
rs1123936	0.82[CEU][hapmap]
rs11603841	0.95[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12794444	0.90[EUR][1000 genomes]
rs1560569	0.91[CEU][hapmap]
rs1569408	0.83[EUR][1000 genomes]
rs16906256	0.82[JPT][hapmap]
rs1883098	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1980428	0.82[CEU][hapmap]
rs1980429	0.83[CEU][hapmap]
rs1988708	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1988709	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2016942	0.91[CEU][hapmap]
rs2455601	0.83[JPT][hapmap]
rs2568031	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2568032	1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2568043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568045	0.82[CEU][hapmap]
rs2568054	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2568059	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568061	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568062	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568065	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568090	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2653567	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2653593	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653605	0.82[CEU][hapmap]
rs2653606	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2653607	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653613	0.86[ASN][1000 genomes]
rs2653616	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742480	0.83[CEU][hapmap]
rs2742536	0.83[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2742537	0.87[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2742540	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2742545	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2742550	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742552	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs34842234	0.84[EUR][1000 genomes]
rs4554887	0.96[EUR][1000 genomes]
rs4909952	0.91[CEU][hapmap]
rs4910062	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4910119	0.81[EUR][1000 genomes]
rs4929911	0.82[CEU][hapmap]
rs4929912	0.82[CEU][hapmap]
rs4929914	0.82[CEU][hapmap]
rs61876187	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6486060	0.83[CEU][hapmap]
rs7119939	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7123429	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7123861	0.85[EUR][1000 genomes]
rs7479407	0.91[CEU][hapmap]
rs7925728	0.91[CEU][hapmap]
rs7930026	0.92[CEU][hapmap]
rs7937298	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7943377	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7945705	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs7947631	0.80[CEU][hapmap]
rs905290	0.82[CEU][hapmap]
rs978636	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1529641	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs1529641	TMEM9B-AS1	cis	lung	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8860600-8864400	Weak transcription	Osteobl	bone
2	chr11:8862000-8864600	Weak transcription	NHDF-Ad	bronchial
3	chr11:8862200-8881200	Weak transcription	Hela-S3	cervix
4	chr11:8862400-8864800	Weak transcription	Fetal Stomach	stomach
5	chr11:8862400-8865000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:8862400-8865000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:8862400-8865000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:8862400-8865200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:8862400-8865200	Weak transcription	Pancreas	Pancrea
10	chr11:8862400-8867000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:8862400-8867800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:8862400-8867800	Weak transcription	Ovary	ovary
13	chr11:8862400-8868000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:8862400-8868000	Weak transcription	Left Ventricle	heart
15	chr11:8862400-8870600	Weak transcription	Placenta	Placenta
16	chr11:8862400-8874600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr11:8862400-8880000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:8862400-8880000	Weak transcription	Spleen	Spleen
19	chr11:8862400-8885000	Weak transcription	NHLF	lung
20	chr11:8862400-8888400	Weak transcription	Right Atrium	heart
21	chr11:8862600-8864400	Weak transcription	A549	lung
22	chr11:8862600-8865200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:8862600-8866400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:8862600-8867000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:8862600-8867800	Weak transcription	Brain Substantia Nigra	brain
26	chr11:8862600-8868400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:8862600-8868800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:8862600-8876600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:8862600-8885200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr11:8862800-8865400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:8863000-8866400	Weak transcription	Fetal Muscle Leg	muscle
32	chr11:8863200-8866400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:8863200-8867200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr11:8863400-8864200	Enhancers	HUVEC	blood vessel
36	chr11:8863600-8864400	Enhancers	Stomach Smooth Muscle	stomach
37	chr11:8863600-8864800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:8863600-8866800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:8863600-8867000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr11:8863800-8865000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:8864000-8864600	Enhancers	Fetal Lung	lung
42	chr11:8864000-8872200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:8864000-8888000	Weak transcription	Fetal Intestine Small	intestine

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