Variant report

Variant	rs3800405
Chromosome Location	chr6:35133228-35133229
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35133125..35135139-chr6:35138368..35141199,2	K562	blood:
2	chr6:35114684..35117968-chr6:35132724..35136247,4	MCF-7	breast:
3	chr6:35132585..35134492-chr6:35202340..35203841,2	MCF-7	breast:
4	chr6:34855546..34857783-chr6:35132391..35134388,2	MCF-7	breast:
5	chr6:35123069..35125917-chr6:35131448..35134859,3	K562	blood:
6	chr6:33697890..33700582-chr6:35133101..35134719,2	MCF-7	breast:
7	chr6:35131417..35136766-chr6:35169545..35174762,6	MCF-7	breast:
8	chr6:35132640..35135454-chr6:35205817..35208602,3	MCF-7	breast:
9	chr6:35127079..35138793-chr6:35145525..35157743,32	MCF-7	breast:
10	chr6:35132639..35135102-chr6:35162466..35164751,2	MCF-7	breast:
11	chr6:35126225..35131731-chr6:35132022..35136988,7	MCF-7	breast:
12	chr6:35132385..35134561-chr6:35180348..35182309,2	MCF-7	breast:
13	chr6:35132111..35134343-chr6:35165160..35168099,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000064999	Chromatin interaction
ENSG00000124678	Chromatin interaction
ENSG00000064995	Chromatin interaction
ENSG00000146197	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1408255	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2005	0.80[JPT][hapmap]
rs3800403	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3800404	0.85[ASN][1000 genomes]
rs4711405	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711407	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457801	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6457802	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6457804	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6457806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911268	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914081	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920194	0.82[ASN][1000 genomes]
rs6925406	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931790	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933979	0.92[YRI][hapmap]
rs6939132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7772251	0.83[JPT][hapmap]
rs9380494	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380495	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9394277	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[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]
rs9394287	0.82[CEU][hapmap]
rs942373	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap]
rs942374	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs942375	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3800405	SCUBE3	cis	parietal	SCAN
rs3800405	UHRF1BP1	cis	parietal	SCAN
rs3800405	GLO1	cis	cerebellum	SCAN
rs3800405	NUDT3	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35128600-35133800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:35128600-35137400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:35128800-35137400	Weak transcription	Brain Angular Gyrus	brain
4	chr6:35130000-35133600	Weak transcription	Fetal Stomach	stomach
5	chr6:35130200-35133400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:35130200-35136000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:35130400-35134000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:35130600-35141400	Weak transcription	Brain Substantia Nigra	brain
9	chr6:35130800-35133400	Enhancers	HepG2	liver
10	chr6:35130800-35136200	Weak transcription	Left Ventricle	heart
11	chr6:35131000-35137400	Weak transcription	Lung	lung
12	chr6:35131200-35133800	Weak transcription	Gastric	stomach
13	chr6:35131800-35134800	Enhancers	Liver	Liver
14	chr6:35131800-35135000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr6:35132200-35134600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:35132200-35134800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr6:35132200-35135600	Enhancers	Stomach Mucosa	stomach
18	chr6:35132400-35134800	Enhancers	Fetal Intestine Large	intestine
19	chr6:35132600-35133800	Weak transcription	Fetal Lung	lung
20	chr6:35132600-35134600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:35132600-35135000	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr6:35132800-35134400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:35132800-35134400	Enhancers	Osteobl	bone
24	chr6:35132800-35134600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:35132800-35134800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:35132800-35134800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr6:35132800-35134800	Enhancers	Fetal Intestine Small	intestine
28	chr6:35132800-35135000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:35133000-35134400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr6:35133000-35134600	Enhancers	NHDF-Ad	bronchial
31	chr6:35133000-35134800	Enhancers	GM12878-XiMat	blood
32	chr6:35133200-35133600	Enhancers	Fetal Kidney	kidney
33	chr6:35133200-35133800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:35133200-35134000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:35133200-35134200	Enhancers	Aorta	Aorta
36	chr6:35133200-35134200	Enhancers	Pancreas	Pancrea
37	chr6:35133200-35134400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:35133200-35134400	Enhancers	NHEK	skin
39	chr6:35133200-35134600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr6:35133200-35134800	Enhancers	Adipose Nuclei	Adipose
41	chr6:35133200-35134800	Enhancers	A549	lung
42	chr6:35133200-35135000	Enhancers	Colonic Mucosa	Colon
43	chr6:35133200-35135000	Enhancers	Esophagus	oesophagus

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