Variant report

Variant	rs6803826
Chromosome Location	chr3:140996969-140996970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140995854..140998314-chr3:141085270..141088004,2	K562	blood:
2	chr3:140948408..140951597-chr3:140996026..140999585,4	MCF-7	breast:
3	chr3:140994584..140997206-chr3:140998045..141000417,2	K562	blood:
4	chr3:140996819..140999221-chr3:141004642..141007259,2	MCF-7	breast:
5	chr3:140991760..140994020-chr3:140996635..140998553,2	K562	blood:
6	chr3:140995281..140996903-chr3:140996967..140998531,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177311	Chromatin interaction
ENSG00000249417	Chromatin interaction
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11715472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1511376	0.81[CEU][hapmap]
rs1511377	0.84[AMR][1000 genomes]
rs1511378	0.83[CEU][hapmap]
rs17204236	1.00[MKK][hapmap]
rs17787670	1.00[LWK][hapmap]
rs1877219	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap]
rs1983234	1.00[LWK][hapmap]
rs1993904	0.84[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2311734	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4683398	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4683588	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs4683592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439985	1.00[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs6439990	0.83[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap]
rs6439993	0.89[CEU][hapmap];0.86[AMR][1000 genomes]
rs6439995	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6803258	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7643346	0.87[GIH][hapmap]
rs899349	0.82[AMR][1000 genomes]
rs9289627	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs9841326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878866	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9880195	1.00[ASW][hapmap];0.94[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][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	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6803826	RNF7	cis	cerebellum	SCAN
rs6803826	ACPL2	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
4	chr3:140978000-140998000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:140979000-141000800	Weak transcription	Fetal Kidney	kidney
6	chr3:140979000-141013200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:140980800-141005600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:140981000-140998400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:140981200-141013200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:140981200-141013400	Weak transcription	Colonic Mucosa	Colon
11	chr3:140981400-141001000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:140983600-141021600	Weak transcription	Esophagus	oesophagus
13	chr3:140984000-140997400	Weak transcription	Fetal Brain Female	brain
14	chr3:140984200-141000800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:140984600-140997600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:140984800-141006400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:140986200-140997600	Weak transcription	Brain Anterior Caudate	brain
18	chr3:140986200-140997600	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:140986200-140997600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:140986200-140998000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:140986200-141000800	Weak transcription	Fetal Lung	lung
22	chr3:140986800-140997400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:140987200-140997400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:140987800-140997600	Weak transcription	HSMMtube	muscle
25	chr3:140988200-141022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:140988400-141001800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:140990800-140998600	Weak transcription	Gastric	stomach
28	chr3:140991000-140997400	Weak transcription	Right Atrium	heart
29	chr3:140991000-140997800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:140991000-140999600	Weak transcription	Pancreas	Pancrea
31	chr3:140992200-140997600	Weak transcription	Brain Angular Gyrus	brain
32	chr3:140993200-141014200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:140993400-140997200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:140993400-140998400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:140993600-140997600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:140993600-141004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:140993800-140997200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:140993800-140997400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:140993800-140997600	Weak transcription	Left Ventricle	heart
40	chr3:140993800-140998400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:140993800-140998600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:140993800-140999600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:140994000-140997000	Weak transcription	Spleen	Spleen
44	chr3:140994000-141006000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:140994200-140997200	Weak transcription	Brain Germinal Matrix	brain
46	chr3:140994200-140997400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:140994200-140997600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:140994200-140997600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:140994200-140997800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:140994200-140999400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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