Variant report

Variant	rs7628692
Chromosome Location	chr3:143082012-143082013
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143079326..143082089-chr3:143083976..143087226,3	K562	blood:
2	chr3:143081768..143084316-chr3:143087882..143089415,2	MCF-7	breast:
3	chr3:143075166..143076875-chr3:143081187..143082787,2	K562	blood:
4	chr3:143076644..143082089-chr3:143083976..143087336,5	K562	blood:
5	chr3:142839497..142841574-chr3:143081300..143083347,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12489162	0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1604378	0.89[CHD][hapmap]
rs4839630	0.89[CHD][hapmap]
rs6777284	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs868702	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs868703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv877564	chr3:143059952-143116883	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877565	chr3:143078986-143116883	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7628692	SLC9A9	cis	parietal	SCAN
rs7628692	ZIC1	cis	cerebellum	SCAN
rs7628692	PLSCR4	cis	parietal	SCAN
rs7628692	PLOD2	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143068200-143091800	Weak transcription	Lung	lung
2	chr3:143070200-143088600	Weak transcription	Aorta	Aorta
3	chr3:143071600-143102400	Weak transcription	Esophagus	oesophagus
4	chr3:143072000-143099400	Weak transcription	Ovary	ovary
5	chr3:143072400-143082200	Weak transcription	Primary B cells from cord blood	blood
6	chr3:143072400-143083000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:143072400-143083000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:143073400-143089600	Weak transcription	Psoas Muscle	Psoas
9	chr3:143077400-143104800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:143080600-143083000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr3:143080800-143082200	Enhancers	NH-A	brain
12	chr3:143080800-143082800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:143080800-143083000	Enhancers	Primary T cells from cord blood	blood
14	chr3:143080800-143083000	Flanking Active TSS	Dnd41	blood
15	chr3:143080800-143083200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:143080800-143083600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:143081000-143083200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr3:143081200-143082200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:143081200-143082200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:143081200-143082400	Enhancers	Fetal Thymus	thymus
21	chr3:143081200-143082800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr3:143081200-143082800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:143081200-143083000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:143081200-143083400	Enhancers	Primary hematopoietic stem cells	blood
25	chr3:143081400-143082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:143081600-143082200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:143081600-143082400	Enhancers	Thymus	Thymus
28	chr3:143081600-143082400	Enhancers	HSMMtube	muscle
29	chr3:143081800-143082400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:143081800-143083200	Enhancers	GM12878-XiMat	blood
31	chr3:143082000-143082200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:143082000-143082200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:143082000-143082200	Flanking Active TSS	K562	blood
34	chr3:143082000-143082400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:143082000-143082800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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