Variant report

Variant	rs11249934
Chromosome Location	chr8:9510830-9510831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10092751	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10094989	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10099122	0.84[ASN][1000 genomes]
rs10102170	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs10109026	0.86[JPT][hapmap]
rs11778555	0.82[EUR][1000 genomes]
rs11782886	0.82[EUR][1000 genomes]
rs11785458	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11785923	0.82[EUR][1000 genomes]
rs12114661	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12155819	0.95[CEU][hapmap];0.98[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12542457	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12542912	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12545250	0.86[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12547642	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12677507	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12679956	0.81[EUR][1000 genomes]
rs12682175	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13263409	0.86[AFR][1000 genomes]
rs13264850	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13272424	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13276086	0.86[CEU][hapmap];0.98[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1394	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33994795	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35316422	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4075359	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4128198	0.86[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4129360	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4422774	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4554469	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4612345	0.82[EUR][1000 genomes]
rs4840426	0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap]
rs4840437	0.82[GIH][hapmap];0.94[TSI][hapmap]
rs4841196	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4841203	0.80[EUR][1000 genomes]
rs4841204	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6601338	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6601340	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6601350	0.81[EUR][1000 genomes]
rs67711814	0.84[EUR][1000 genomes]
rs6982148	0.95[CEU][hapmap];0.80[AMR][1000 genomes]
rs6990300	0.83[ASW][hapmap];0.98[GIH][hapmap]
rs6990418	0.86[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6992666	0.81[EUR][1000 genomes]
rs6994574	0.95[CEU][hapmap];0.98[GIH][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7004937	0.86[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7006985	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73202879	0.85[ASN][1000 genomes]
rs7461939	0.95[CEU][hapmap];0.98[GIH][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7462070	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7822700	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7835002	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7840706	0.86[AFR][1000 genomes]
rs7846399	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9644704	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9644707	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv497927	chr8:9097611-9544519	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11249934	C8orf13	cis	multi-tissue	Pritchard
rs11249934	CLDN23	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9495800-9531000	Weak transcription	Gastric	stomach
2	chr8:9499800-9512400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr8:9501200-9511200	Weak transcription	Right Atrium	heart
4	chr8:9501600-9511000	Weak transcription	Ovary	ovary
5	chr8:9501600-9511400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr8:9501600-9525400	Weak transcription	Thymus	Thymus
7	chr8:9501800-9528400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr8:9501800-9534400	Weak transcription	Fetal Heart	heart
9	chr8:9502800-9511000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr8:9503000-9521200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr8:9504200-9529400	Weak transcription	Colon Smooth Muscle	Colon
12	chr8:9504400-9512200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr8:9504800-9549600	Weak transcription	Pancreas	Pancrea
14	chr8:9506000-9521200	Weak transcription	Aorta	Aorta
15	chr8:9506400-9530200	Weak transcription	HepG2	liver
16	chr8:9507600-9511400	Enhancers	NHDF-Ad	bronchial
17	chr8:9507800-9529400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr8:9508000-9511600	Enhancers	Osteobl	bone
19	chr8:9508000-9512600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr8:9508200-9512200	Weak transcription	Fetal Thymus	thymus
21	chr8:9508400-9521200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr8:9509000-9513200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr8:9509000-9513400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:9509000-9514000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr8:9509200-9511600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr8:9509200-9512200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr8:9509200-9512400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr8:9509200-9522400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr8:9509400-9511000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr8:9509400-9511200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr8:9509400-9511400	Weak transcription	Brain Substantia Nigra	brain
32	chr8:9509400-9511400	Weak transcription	Fetal Lung	lung
33	chr8:9509400-9512200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr8:9509400-9512200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr8:9509400-9512400	Weak transcription	Adipose Nuclei	Adipose
36	chr8:9509400-9512400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr8:9509400-9512600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr8:9509400-9512800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr8:9509400-9513400	Weak transcription	HSMMtube	muscle
40	chr8:9509400-9513600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr8:9509400-9516000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr8:9509400-9523000	Weak transcription	Brain Anterior Caudate	brain
43	chr8:9509400-9545000	Weak transcription	HSMM	muscle
44	chr8:9509600-9513600	Weak transcription	HMEC	breast
45	chr8:9509600-9529400	Weak transcription	Spleen	Spleen
46	chr8:9509600-9532000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr8:9509800-9511200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr8:9509800-9512400	Weak transcription	Lung	lung
49	chr8:9510000-9511200	Weak transcription	NHEK	skin
50	chr8:9510000-9528800	Weak transcription	Stomach Smooth Muscle	stomach

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