Variant report

Variant	rs9444484
Chromosome Location	chr6:87939964-87939965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1980790	1.00[YRI][hapmap]
rs1980792	1.00[YRI][hapmap]
rs2147921	1.00[YRI][hapmap]
rs3857488	1.00[YRI][hapmap]
rs3904088	1.00[YRI][hapmap]
rs4707358	1.00[YRI][hapmap]
rs6909200	1.00[YRI][hapmap]
rs6926831	1.00[YRI][hapmap]
rs7739034	1.00[YRI][hapmap]
rs7757827	1.00[YRI][hapmap]
rs7758618	1.00[YRI][hapmap]
rs7766324	1.00[YRI][hapmap]
rs7768575	1.00[YRI][hapmap]
rs9344693	1.00[YRI][hapmap]
rs9351117	1.00[YRI][hapmap]
rs9353462	1.00[YRI][hapmap]
rs9353464	1.00[YRI][hapmap]

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	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
3	nsv349799	chr6:87939951-87939964	Strong transcription Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9444484	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9444484	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx
rs9444484	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs9444484	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs9444484	C6orf164	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87884000-87964400	Weak transcription	NHEK	skin
2	chr6:87888200-87964200	Weak transcription	HSMMtube	muscle
3	chr6:87891000-87956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:87905200-87950200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:87906200-87956200	Weak transcription	A549	lung
6	chr6:87906400-87964400	Weak transcription	NHLF	lung
7	chr6:87910600-87956000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:87920000-87945400	Strong transcription	Dnd41	blood
9	chr6:87922200-87956200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:87923200-87953600	Weak transcription	Stomach Mucosa	stomach
11	chr6:87923200-87956000	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:87923400-87955600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:87923400-87956200	Weak transcription	Gastric	stomach
14	chr6:87923400-87956200	Weak transcription	Small Intestine	intestine
15	chr6:87923400-87969000	Weak transcription	Psoas Muscle	Psoas
16	chr6:87924000-87956200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:87924400-87966000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:87924600-87956200	Weak transcription	Right Ventricle	heart
19	chr6:87925600-87940200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr6:87925600-87948200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:87926000-87940000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:87926200-87940000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:87926200-87943200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:87926800-87940000	Strong transcription	Primary B cells from cord blood	blood
25	chr6:87928000-87956200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:87929200-87940200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:87930600-87954000	Weak transcription	HMEC	breast
28	chr6:87931200-87952400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:87932400-87940200	Strong transcription	GM12878-XiMat	blood
30	chr6:87933200-87956200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:87933400-87950200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:87933600-87940000	Strong transcription	Placenta	Placenta
33	chr6:87933600-87945000	Weak transcription	Fetal Intestine Small	intestine
34	chr6:87933600-87948000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:87933600-87948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:87933600-87948600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:87933600-87948600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:87933600-87948800	Weak transcription	Ovary	ovary
39	chr6:87933600-87949600	Weak transcription	Fetal Stomach	stomach
40	chr6:87933600-87951200	Weak transcription	Pancreas	Pancrea
41	chr6:87933600-87956200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr6:87933600-87956200	Weak transcription	Lung	lung
43	chr6:87933600-87956400	Weak transcription	Esophagus	oesophagus
44	chr6:87933800-87944600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr6:87933800-87956200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:87933800-87956200	Weak transcription	Colonic Mucosa	Colon
47	chr6:87934000-87947000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:87934000-87948800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:87934000-87956200	Weak transcription	Left Ventricle	heart
50	chr6:87934000-87956400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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