Variant report

Variant	rs10869401
Chromosome Location	chr9:71457783-71457784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10511962	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511963	0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs10781227	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781245	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10869335	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs10869360	0.81[AMR][1000 genomes]
rs10869365	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10869395	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10869396	0.93[ASW][hapmap];0.92[CEU][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10869400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869403	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10869407	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10869419	0.84[CEU][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10869541	0.81[CHD][hapmap]
rs10869574	0.82[CHB][hapmap]
rs11792022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414944	0.87[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1414949	0.83[MEX][hapmap]
rs2017	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2027025	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2027205	0.87[CHB][hapmap]
rs2152649	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs4145885	0.80[AFR][1000 genomes]
rs4237270	0.87[MEX][hapmap]
rs4375069	0.86[CHB][hapmap]
rs4744726	0.87[MEX][hapmap]
rs4745295	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4745296	0.91[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.90[YRI][hapmap];0.91[ASN][1000 genomes]
rs6560391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6560392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018692	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7031640	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7033278	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7043133	0.91[MEX][hapmap]
rs7851923	0.86[MEX][hapmap]
rs7856247	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7857352	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7863342	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7867240	0.87[CHB][hapmap]
rs7874714	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs944856	0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9776840	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv6548	chr9:71429527-71470917	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10869401	TJP2	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71435800-71464800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:71438000-71491200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:71440600-71466600	Weak transcription	Gastric	stomach
4	chr9:71441000-71478600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:71441600-71459800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:71443600-71458600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr9:71443600-71459000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr9:71445600-71458600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:71448200-71485600	Weak transcription	Stomach Mucosa	stomach
10	chr9:71449200-71459200	Weak transcription	Primary B cells from cord blood	blood
11	chr9:71452000-71458400	Weak transcription	Spleen	Spleen
12	chr9:71452200-71458000	Weak transcription	Lung	lung
13	chr9:71453800-71458600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:71455800-71459400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr9:71456000-71457800	Weak transcription	Fetal Intestine Large	intestine
16	chr9:71456000-71458000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr9:71456000-71458000	Enhancers	GM12878-XiMat	blood
18	chr9:71456800-71460000	Strong transcription	Fetal Intestine Small	intestine
19	chr9:71456800-71460600	Enhancers	Left Ventricle	heart
20	chr9:71457000-71457800	Enhancers	Brain Angular Gyrus	brain
21	chr9:71457200-71458400	Weak transcription	Right Ventricle	heart
22	chr9:71457200-71458600	Weak transcription	Brain Anterior Caudate	brain
23	chr9:71457200-71458800	Weak transcription	Right Atrium	heart
24	chr9:71457200-71458800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr9:71457200-71459000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:71457200-71459400	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:71457400-71457800	Weak transcription	Aorta	Aorta
28	chr9:71457400-71459800	Weak transcription	Fetal Heart	heart
29	chr9:71457600-71458200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr9:71457600-71459200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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