Variant report

Variant	rs6675606
Chromosome Location	chr1:226236712-226236713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226235405..226240206-chr1:226241102..226244494,5	MCF-7	breast:
2	chr1:226234724..226236759-chr1:226248520..226251934,3	MCF-7	breast:
3	chr1:226232126..226234237-chr1:226235651..226237839,2	MCF-7	breast:
4	chr1:226195886..226198130-chr1:226234850..226237174,2	K562	blood:

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction
ENSG00000272562	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10157179	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10753411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799333	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10799334	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10915920	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10915921	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915924	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915927	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12128917	0.90[EUR][1000 genomes]
rs12728713	0.82[GIH][hapmap]
rs12743653	0.82[GIH][hapmap]
rs1877158	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2001307	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4477241	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4604663	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653438	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653439	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653703	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653704	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653705	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653706	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426096	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6426098	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6426099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6682659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6693325	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6701318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73100558	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7550220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7553984	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9701639	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription 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 miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv523155	chr1:226234883-226239830	Weak transcription Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
3	nsv524575	chr1:226234883-226242772	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6675606	FBXO28	cis	cerebellum	SCAN
rs6675606	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs6675606	H3F3A	cis	Esophagus Mucosa	GTEx
rs6675606	H3F3A	cis	Nerve Tibial	GTEx
rs6675606	H3F3A	cis	Artery Tibial	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226222400-226242200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:226222600-226241400	Weak transcription	Liver	Liver
3	chr1:226222600-226242600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:226222600-226248600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:226223000-226242000	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:226223800-226238400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:226223800-226242400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:226225400-226242400	Weak transcription	Fetal Brain Female	brain
9	chr1:226226000-226248000	Weak transcription	Left Ventricle	heart
10	chr1:226228800-226242200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:226229600-226241800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:226229600-226248200	Weak transcription	Brain Germinal Matrix	brain
13	chr1:226229800-226249400	Weak transcription	Spleen	Spleen
14	chr1:226230000-226249200	Weak transcription	Aorta	Aorta
15	chr1:226231000-226241600	Weak transcription	Fetal Thymus	thymus
16	chr1:226231200-226242200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:226231200-226242400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:226231200-226249200	Weak transcription	Pancreas	Pancrea
19	chr1:226232000-226249200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:226232200-226249400	Weak transcription	Gastric	stomach
21	chr1:226232600-226248600	Weak transcription	Brain Substantia Nigra	brain
22	chr1:226232800-226242000	Weak transcription	Thymus	Thymus
23	chr1:226234600-226243400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:226234600-226248000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:226234600-226248800	Weak transcription	HSMM	muscle
26	chr1:226234800-226248800	Weak transcription	HSMMtube	muscle
27	chr1:226235000-226238000	Weak transcription	Primary T cells from cord blood	blood
28	chr1:226235000-226248200	Weak transcription	Fetal Intestine Large	intestine
29	chr1:226235000-226248800	Weak transcription	Colonic Mucosa	Colon
30	chr1:226235200-226246200	Weak transcription	Fetal Lung	lung
31	chr1:226235200-226248600	Weak transcription	HepG2	liver
32	chr1:226235200-226249200	Weak transcription	Small Intestine	intestine
33	chr1:226235400-226241000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:226235400-226248000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:226235400-226248600	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:226235400-226249200	Weak transcription	Esophagus	oesophagus
37	chr1:226235600-226242000	Weak transcription	Adipose Nuclei	Adipose
38	chr1:226235600-226242200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:226235600-226243400	Weak transcription	Brain Anterior Caudate	brain
40	chr1:226235600-226248200	Weak transcription	Fetal Intestine Small	intestine
41	chr1:226235800-226238000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:226235800-226238200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr1:226235800-226238400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr1:226235800-226239800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:226235800-226240600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:226235800-226240800	Weak transcription	Primary B cells from cord blood	blood
47	chr1:226235800-226241800	Weak transcription	Placenta	Placenta
48	chr1:226235800-226242200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:226235800-226242200	Weak transcription	Lung	lung
50	chr1:226235800-226246200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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