Variant report

Variant	rs6601340
Chromosome Location	chr8:9461315-9461316
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10092751	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10094989	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs10102170	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs10109026	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs11249934	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs11778555	0.82[EUR][1000 genomes]
rs11782886	0.82[EUR][1000 genomes]
rs11785458	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11785923	0.82[EUR][1000 genomes]
rs12114661	0.82[EUR][1000 genomes]
rs12155819	0.95[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs12541617	0.81[YRI][hapmap]
rs12542457	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs12542912	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs12543959	0.83[YRI][hapmap]
rs12545250	0.86[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12547642	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12677507	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12679956	0.83[EUR][1000 genomes]
rs12682175	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13263409	0.86[YRI][hapmap]
rs13264850	0.82[EUR][1000 genomes]
rs13270518	0.90[YRI][hapmap]
rs13272424	0.82[EUR][1000 genomes]
rs13276086	0.86[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs1394	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs33994795	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35316422	0.82[EUR][1000 genomes]
rs4075359	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4128198	0.86[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4129360	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs4422774	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4554469	0.89[EUR][1000 genomes]
rs4612345	0.83[EUR][1000 genomes]
rs4840425	0.81[AMR][1000 genomes]
rs4840426	0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4840437	0.86[TSI][hapmap]
rs4841196	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4841203	0.82[EUR][1000 genomes]
rs4841204	0.82[EUR][1000 genomes]
rs6601327	0.82[YRI][hapmap]
rs6601338	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6601350	0.80[EUR][1000 genomes]
rs67711814	0.84[EUR][1000 genomes]
rs6982148	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs6990300	0.84[MEX][hapmap]
rs6990418	0.86[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6992666	0.83[EUR][1000 genomes]
rs6994574	0.95[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs7004937	0.86[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7006985	0.80[EUR][1000 genomes]
rs7460484	0.80[ASN][1000 genomes]
rs7461939	0.95[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs7462070	0.82[EUR][1000 genomes]
rs7822700	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs7835002	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7840706	0.83[YRI][hapmap]
rs7846399	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9644704	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs9644707	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv1797711	chr8:9456376-9462653	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6601340	CLDN23	cis	multi-tissue	Pritchard
rs6601340	C8orf13	cis	multi-tissue	Pritchard

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9428200-9466200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:9435400-9465600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:9435400-9468400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr8:9435600-9472400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr8:9435800-9465400	Weak transcription	Lung	lung
6	chr8:9435800-9465600	Weak transcription	Pancreas	Pancrea
7	chr8:9435800-9472600	Weak transcription	HSMMtube	muscle
8	chr8:9437400-9468000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr8:9439400-9472400	Weak transcription	HSMM	muscle
10	chr8:9439600-9465600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr8:9440600-9465600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr8:9442600-9465400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr8:9447600-9465400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:9449200-9465600	Weak transcription	Ovary	ovary
15	chr8:9450200-9465600	Weak transcription	NHDF-Ad	bronchial
16	chr8:9450200-9470600	Weak transcription	NHLF	lung
17	chr8:9450200-9472200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr8:9450600-9469600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr8:9450600-9480200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr8:9450800-9462600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr8:9450800-9462800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr8:9450800-9464400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr8:9450800-9465400	Weak transcription	Left Ventricle	heart
24	chr8:9450800-9468400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr8:9450800-9471000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr8:9451200-9461800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr8:9453400-9465400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr8:9454600-9465600	Weak transcription	Psoas Muscle	Psoas
29	chr8:9454800-9466000	Weak transcription	Brain Angular Gyrus	brain
30	chr8:9455200-9462200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr8:9455400-9462600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr8:9455400-9470600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr8:9455400-9471800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr8:9457000-9465800	Weak transcription	Colon Smooth Muscle	Colon
35	chr8:9457000-9470400	Weak transcription	Small Intestine	intestine
36	chr8:9459000-9465400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr8:9459600-9462200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr8:9459800-9461400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr8:9460000-9465800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr8:9460000-9469600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr8:9460200-9461600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:9460200-9462600	Weak transcription	Primary B cells from cord blood	blood
43	chr8:9460200-9470600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr8:9460600-9461400	ZNF genes & repeats	Dnd41	blood
45	chr8:9461000-9463000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
46	chr8:9461000-9470800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr8:9461000-9486400	Weak transcription	Fetal Intestine Small	intestine
48	chr8:9461200-9462000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr8:9461200-9463800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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