Variant report

Variant	rs7819412
Chromosome Location	chr8:11045161-11045162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11042678..11045323-chr8:11057984..11059952,2	MCF-7	breast:
2	chr8:11040791..11043774-chr8:11044879..11047578,2	K562	blood:

Variant related genes	Relation type
ENSG00000171044	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10087081	0.82[CHB][hapmap]
rs10093053	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10106914	0.82[CHB][hapmap]
rs10108347	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10109167	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10503416	0.82[CHB][hapmap]
rs11250119	1.00[JPT][hapmap];0.81[TSI][hapmap]
rs11250121	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17724467	0.82[CHB][hapmap]
rs17783634	0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2409710	0.82[CHB][hapmap]
rs2409712	0.82[CHB][hapmap]
rs2409718	0.87[ASW][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs2409722	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2409724	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2409742	0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28633434	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3021494	0.87[ASW][hapmap];0.82[CHB][hapmap]
rs4333549	0.82[CHB][hapmap]
rs4523214	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4840551	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs4841495	0.82[JPT][hapmap]
rs4841498	0.82[CHB][hapmap]
rs4841500	0.82[CHB][hapmap]
rs4841507	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6601560	0.82[CEU][hapmap]
rs6601564	0.82[CHB][hapmap]
rs6601565	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601570	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6981523	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6986032	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7004825	0.85[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7010590	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7813802	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1026331	chr8:10955941-11046394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Triglycerides	19060906	GWAS catalog

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7819412	CLDN23	cis	multi-tissue	Pritchard
rs7819412	PRSS55	cis	cerebellum	SCAN
rs7819412	TDH	cis	cerebellum	SCAN
rs7819412	C8orf5	cis	normal skin	skin_eQTL
rs7819412	FLJ10661	cis	cerebellum	SCAN
rs7819412	TDH	cis	parietal	SCAN
rs7819412	C8orf48	cis	cerebellum	SCAN
rs7819412	MFHAS1	cis	cerebellum	SCAN
rs7819412	CTSB	cis	cerebellum	SCAN
rs7819412	C8orf13	cis	multi-tissue	Pritchard
rs7819412	AF131215.2	cis	Nerve Tibial	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11028000-11048200	Weak transcription	Primary B cells from cord blood	blood
2	chr8:11028200-11050200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr8:11028200-11052400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr8:11028200-11056600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr8:11028800-11054400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:11029600-11056800	Weak transcription	Fetal Intestine Small	intestine
7	chr8:11031400-11054200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr8:11032000-11053800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr8:11034600-11054400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr8:11034600-11057000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr8:11034600-11057000	Weak transcription	Esophagus	oesophagus
12	chr8:11035400-11054600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr8:11035600-11054000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:11035800-11051600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr8:11035800-11056000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr8:11039400-11052200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr8:11040000-11045400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr8:11040600-11054200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr8:11040800-11050000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr8:11041000-11051600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr8:11041600-11054200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:11042200-11055000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr8:11042600-11046000	Enhancers	Fetal Brain Male	brain
24	chr8:11042800-11056600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr8:11043000-11046800	Enhancers	HSMMtube	muscle
26	chr8:11043800-11045600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:11043800-11046400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr8:11044200-11046600	Enhancers	Osteobl	bone
29	chr8:11044400-11045200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr8:11044400-11045600	Weak transcription	GM12878-XiMat	blood
31	chr8:11044400-11046200	Weak transcription	Spleen	Spleen
32	chr8:11044600-11045200	Enhancers	Fetal Stomach	stomach
33	chr8:11044600-11045200	Enhancers	Rectal Smooth Muscle	rectum
34	chr8:11044600-11045600	Enhancers	NHEK	skin
35	chr8:11044600-11046200	Enhancers	NH-A	brain
36	chr8:11044600-11046600	Enhancers	HSMM	muscle
37	chr8:11044800-11045600	Enhancers	Psoas Muscle	Psoas
38	chr8:11044800-11046000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr8:11044800-11054800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr8:11045000-11045400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr8:11045000-11045400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr8:11045000-11046200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr8:11045000-11046400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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