Variant report

Variant	rs4706290
Chromosome Location	chr6:87917583-87917584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:87863031..87865644-chr6:87916058..87917647,2	K562	blood:
2	chr6:87912583..87915410-chr6:87916738..87919725,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272008	Chromatin interaction
ENSG00000188994	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13194868	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1328477	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2240461	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2274582	0.87[EUR][1000 genomes]
rs2875533	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4707349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60992482	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7773715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294366	0.82[CEU][hapmap]
rs932742	0.87[CEU][hapmap]
rs9444485	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450629	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450659	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4706290	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs4706290	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87868000-87933000	Weak transcription	Hela-S3	cervix
2	chr6:87874400-87924200	Weak transcription	Fetal Kidney	kidney
3	chr6:87879800-87923000	Weak transcription	Esophagus	oesophagus
4	chr6:87881400-87926200	Weak transcription	Liver	Liver
5	chr6:87883400-87926200	Weak transcription	Fetal Lung	lung
6	chr6:87884000-87964400	Weak transcription	NHEK	skin
7	chr6:87888200-87964200	Weak transcription	HSMMtube	muscle
8	chr6:87889800-87926400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:87890800-87933000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:87891000-87920000	Weak transcription	Placenta	Placenta
11	chr6:87891000-87956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:87891200-87929200	Weak transcription	Thymus	Thymus
13	chr6:87891400-87932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:87892000-87923000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:87892800-87921600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:87893000-87917600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:87894800-87921800	Weak transcription	NHDF-Ad	bronchial
18	chr6:87894800-87924200	Weak transcription	Adipose Nuclei	Adipose
19	chr6:87894800-87926200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:87895800-87924000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:87896000-87932800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:87896200-87920200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:87896200-87921400	Weak transcription	HepG2	liver
24	chr6:87896400-87925600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:87896400-87926000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:87896400-87927400	Weak transcription	HMEC	breast
27	chr6:87896400-87927800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:87896600-87923200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:87896600-87925600	Weak transcription	HSMM	muscle
30	chr6:87905200-87950200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:87906200-87921800	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:87906200-87956200	Weak transcription	A549	lung
33	chr6:87906400-87917600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:87906400-87919200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:87906400-87920200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:87906400-87964400	Weak transcription	NHLF	lung
37	chr6:87907400-87930800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:87907800-87929200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr6:87908800-87918800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:87909000-87928400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:87909000-87929800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:87909800-87918600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:87909800-87918600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:87909800-87918600	Weak transcription	Small Intestine	intestine
45	chr6:87909800-87921600	Weak transcription	Gastric	stomach
46	chr6:87910200-87934400	Weak transcription	Fetal Brain Male	brain
47	chr6:87910400-87921800	Weak transcription	Brain Substantia Nigra	brain
48	chr6:87910400-87922000	Weak transcription	Brain Angular Gyrus	brain
49	chr6:87910400-87922400	Weak transcription	Brain Germinal Matrix	brain
50	chr6:87910400-87922600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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