Variant report

Variant	rs11042099
Chromosome Location	chr11:8867342-8867343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10734638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10840127	0.95[CEU][hapmap]
rs10840129	0.94[CEU][hapmap]
rs1133833	1.00[CEU][hapmap]
rs16906056	0.89[CEU][hapmap]
rs16906614	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17337866	0.95[CEU][hapmap]
rs1811367	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2060157	0.84[EUR][1000 genomes]
rs2568029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2568056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2568078	0.90[EUR][1000 genomes]
rs2653558	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2653566	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653618	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2742483	0.82[EUR][1000 genomes]
rs2742502	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2742549	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742553	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34023999	0.85[AMR][1000 genomes]
rs34033747	0.87[AMR][1000 genomes]
rs34152382	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34275210	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34371023	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34418236	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34581555	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34769330	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35503692	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35563381	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35580466	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35909878	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36094920	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36100955	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36180552	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3850934	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs3915868	0.89[CEU][hapmap];0.81[AMR][1000 genomes]
rs4910068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7117900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127197	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7950491	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11042099	C11orf17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8862200-8881200	Weak transcription	Hela-S3	cervix
2	chr11:8862400-8867800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:8862400-8867800	Weak transcription	Ovary	ovary
4	chr11:8862400-8868000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:8862400-8868000	Weak transcription	Left Ventricle	heart
6	chr11:8862400-8870600	Weak transcription	Placenta	Placenta
7	chr11:8862400-8874600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr11:8862400-8880000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:8862400-8880000	Weak transcription	Spleen	Spleen
10	chr11:8862400-8885000	Weak transcription	NHLF	lung
11	chr11:8862400-8888400	Weak transcription	Right Atrium	heart
12	chr11:8862600-8867800	Weak transcription	Brain Substantia Nigra	brain
13	chr11:8862600-8868400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:8862600-8868800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:8862600-8876600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:8862600-8885200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr11:8864000-8872200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:8864000-8888000	Weak transcription	Fetal Intestine Small	intestine
20	chr11:8865400-8867600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:8865400-8873600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:8865600-8867600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:8865800-8867600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr11:8865800-8886000	Weak transcription	Fetal Stomach	stomach
25	chr11:8866000-8874200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:8866400-8867400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:8867000-8867400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:8867000-8867600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:8867000-8867800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:8867000-8867800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:8867200-8867600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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