Variant report

Variant	rs6780280
Chromosome Location	chr3:143179870-143179871
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	chr3:143179159..143180857-chr3:143180887..143183705,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10212321	0.99[ASN][1000 genomes]
rs10212557	0.99[ASN][1000 genomes]
rs1097938	0.99[ASN][1000 genomes]
rs1097939	0.99[ASN][1000 genomes]
rs1097940	0.99[ASN][1000 genomes]
rs12486916	0.82[EUR][1000 genomes]
rs12488945	0.82[EUR][1000 genomes]
rs12490020	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1525010	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525011	0.92[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530215	0.99[ASN][1000 genomes]
rs1530216	0.99[ASN][1000 genomes]
rs1660477	0.99[ASN][1000 genomes]
rs1660481	0.99[ASN][1000 genomes]
rs16853629	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723028	0.99[ASN][1000 genomes]
rs1723031	0.99[ASN][1000 genomes]
rs1723034	0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs1852059	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1899217	0.81[EUR][1000 genomes]
rs1978912	0.99[ASN][1000 genomes]
rs2165360	0.82[EUR][1000 genomes]
rs2582353	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2582354	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs57914974	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60765365	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66508148	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66599925	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs66925722	0.81[EUR][1000 genomes]
rs6768834	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779984	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793614	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802358	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs6804097	0.84[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716748	0.99[ASN][1000 genomes]
rs838606	0.84[CHD][hapmap];0.80[JPT][hapmap]
rs838609	0.99[ASN][1000 genomes]
rs838610	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs838611	0.99[ASN][1000 genomes]
rs838612	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs838614	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs838615	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs838617	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs838619	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs838621	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs838624	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs838625	0.94[ASN][1000 genomes]
rs838626	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[ASN][1000 genomes]
rs838629	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[ASN][1000 genomes]
rs838640	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs838641	0.91[ASN][1000 genomes]
rs838647	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs865709	0.99[ASN][1000 genomes]
rs9289663	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6780280	RNF7	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143159600-143200800	Weak transcription	Esophagus	oesophagus
2	chr3:143163400-143181400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:143163400-143196800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:143163600-143184000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:143163600-143187000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:143163800-143183600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:143163800-143196400	Weak transcription	Fetal Stomach	stomach
8	chr3:143163800-143203400	Weak transcription	Ovary	ovary
9	chr3:143170000-143184400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:143170400-143181400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr3:143170400-143185200	Weak transcription	Primary B cells from cord blood	blood
12	chr3:143174400-143220400	Weak transcription	Fetal Lung	lung
13	chr3:143176800-143220400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:143177200-143200800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:143177400-143184600	Weak transcription	Adipose Nuclei	Adipose
16	chr3:143177600-143183200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:143177800-143204400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:143178000-143203200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:143179400-143185000	Weak transcription	Primary T cells from cord blood	blood
20	chr3:143179400-143220400	Weak transcription	Brain Substantia Nigra	brain
21	chr3:143179800-143185600	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:143179800-143213400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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