Variant report

Variant	rs1711564
Chromosome Location	chr3:99422587-99422588
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:99421172-99422723	ProgFib	skin:	n/a	n/a
2	POLR2A	chr3:99417105-99422755	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:55802636..55803304-chr3:99422573..99423568,2	MCF-7	breast:

Variant related genes	Relation type
COL8A1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10935917	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs1610509	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1708167	0.98[ASN][1000 genomes]
rs1711554	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1718235	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs497868	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs498411	0.98[ASN][1000 genomes]
rs652026	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs669676	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs704571	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs704572	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs704574	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7629046	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs792831	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs792833	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs792835	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs792836	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs792837	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs793482	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs793483	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs793485	0.95[CHB][hapmap]
rs793502	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs813218	0.82[LWK][hapmap];0.85[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1711564	ZPLD1	cis	parietal	SCAN
rs1711564	IMPG2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99394000-99426600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:99397600-99432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:99403600-99424800	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:99411400-99439600	Weak transcription	NHEK	skin
5	chr3:99411800-99426000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:99413000-99423400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:99413600-99422800	Weak transcription	HMEC	breast
8	chr3:99413800-99423800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:99417800-99423800	Genic enhancers	Muscle Satellite Cultured Cells	--
10	chr3:99419000-99428200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:99419600-99422600	Genic enhancers	NH-A	brain
12	chr3:99419800-99423600	Weak transcription	Aorta	Aorta
13	chr3:99419800-99430400	Weak transcription	Left Ventricle	heart
14	chr3:99420000-99427000	Weak transcription	Right Atrium	heart
15	chr3:99420000-99428800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:99420000-99429400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:99420000-99432800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:99420000-99433000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:99420600-99430400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:99421000-99427200	Strong transcription	HUVEC	blood vessel
21	chr3:99421200-99422600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:99421800-99422600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:99421800-99422600	Enhancers	Rectal Smooth Muscle	rectum
24	chr3:99422000-99422600	Enhancers	Fetal Lung	lung
25	chr3:99422200-99423800	Enhancers	Adipose Nuclei	Adipose
26	chr3:99422200-99426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:99422400-99423400	Strong transcription	Osteobl	bone
28	chr3:99422400-99424000	Weak transcription	NHDF-Ad	bronchial
29	chr3:99422400-99425200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:99422400-99425800	Weak transcription	NHLF	lung
31	chr3:99422400-99426200	Strong transcription	HSMM	muscle
32	chr3:99422400-99426200	Weak transcription	HSMMtube	muscle

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