Variant report

Variant	rs9561932
Chromosome Location	chr13:96347177-96347178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96327692..96330287-chr13:96346205..96350903,4	K562	blood:
2	chr13:96329213..96330784-chr13:96346091..96348298,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102580	Chromatin interaction
ENSG00000247400	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11070154	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap]
rs11616456	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11619004	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12858210	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs12876018	0.85[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap]
rs1537030	0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap]
rs2389372	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3087339	0.91[YRI][hapmap]
rs3125431	0.91[YRI][hapmap]
rs3848074	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4773928	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs6492817	0.84[LWK][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs6492824	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs7323150	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs7327549	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329098	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7338859	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs7981593	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7981923	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs7995045	0.86[AFR][1000 genomes]
rs7995306	0.91[ASW][hapmap];0.81[LWK][hapmap];0.95[YRI][hapmap]
rs9302086	0.91[YRI][hapmap]
rs9556503	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs9556504	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs9561935	0.91[ASW][hapmap];0.88[LWK][hapmap];0.80[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs9561936	0.80[TSI][hapmap]
rs9561948	0.91[YRI][hapmap]
rs9561951	0.91[YRI][hapmap]
rs9561964	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs9561967	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs9561969	0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap]
rs9590313	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9590318	0.84[LWK][hapmap];0.95[YRI][hapmap]
rs9590321	0.82[LWK][hapmap];1.00[YRI][hapmap]

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	nsv832690	chr13:96330757-96508077	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv974118	chr13:96346708-96351488	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9561932	CLDN10	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96331400-96350600	Weak transcription	Aorta	Aorta
2	chr13:96331400-96362200	Weak transcription	HSMM	muscle
3	chr13:96332000-96348000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:96332400-96360400	Weak transcription	NHDF-Ad	bronchial
5	chr13:96332600-96350200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr13:96337400-96347600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr13:96337400-96350400	Weak transcription	Lung	lung
8	chr13:96337600-96347200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:96337600-96347800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:96337600-96348400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:96337600-96350400	Weak transcription	Pancreas	Pancrea
12	chr13:96337600-96350400	Weak transcription	Right Ventricle	heart
13	chr13:96337600-96350400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr13:96337600-96350400	Weak transcription	Small Intestine	intestine
15	chr13:96337600-96356000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:96337600-96358800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr13:96337600-96360800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr13:96337600-96362200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr13:96337600-96364200	Weak transcription	Ovary	ovary
20	chr13:96341000-96350600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr13:96341200-96350400	Weak transcription	Psoas Muscle	Psoas
22	chr13:96341200-96350400	Weak transcription	Right Atrium	heart
23	chr13:96342000-96350400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr13:96342000-96350400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr13:96342000-96350600	Weak transcription	Liver	Liver
26	chr13:96342200-96349200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr13:96344200-96348200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr13:96345000-96352600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr13:96345200-96362200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr13:96345800-96347800	Weak transcription	Fetal Lung	lung
31	chr13:96346400-96348600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr13:96346400-96350200	Weak transcription	Fetal Heart	heart
33	chr13:96346600-96350000	ZNF genes & repeats	GM12878-XiMat	blood
34	chr13:96346600-96350600	Weak transcription	Brain Anterior Caudate	brain
35	chr13:96346800-96348600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr13:96346800-96349600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr13:96347000-96347400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
38	chr13:96347000-96348600	ZNF genes & repeats	Primary T cells from cord blood	blood
39	chr13:96347000-96348600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:96347000-96349200	Weak transcription	Adipose Nuclei	Adipose
41	chr13:96347000-96351000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:96347000-96377600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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