Variant report

Variant	rs7621298
Chromosome Location	chr3:43383641-43383642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:43383468-43384599	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SNRK	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10865932	0.82[JPT][hapmap]
rs11130004	0.90[GIH][hapmap]
rs12485977	0.89[AMR][1000 genomes]
rs12492694	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs13095863	0.91[ASW][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs13320571	0.82[JPT][hapmap]
rs1351631	0.90[GIH][hapmap]
rs1384435	0.90[GIH][hapmap]
rs1564434	0.90[GIH][hapmap]
rs1588026	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17075317	1.00[JPT][hapmap]
rs17075335	0.85[JPT][hapmap]
rs17075597	0.82[JPT][hapmap]
rs1975997	0.90[GIH][hapmap]
rs2101064	0.88[GIH][hapmap]
rs4128530	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4407383	0.93[GIH][hapmap]
rs4547674	0.93[GIH][hapmap]
rs4682685	0.82[JPT][hapmap]
rs4682882	0.82[JPT][hapmap]
rs4683364	0.85[JPT][hapmap]
rs4683366	1.00[JPT][hapmap]
rs6441772	0.82[JPT][hapmap]
rs6769576	0.93[GIH][hapmap]
rs6781696	0.85[JPT][hapmap]
rs6791641	0.82[JPT][hapmap]
rs6793392	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6803929	0.82[JPT][hapmap]
rs737516	0.90[GIH][hapmap]
rs9311340	0.90[GIH][hapmap]
rs9681394	1.00[JPT][hapmap]
rs9683242	1.00[JPT][hapmap]
rs9815196	0.90[GIH][hapmap]
rs9820946	0.84[JPT][hapmap]
rs9858494	0.81[AFR][1000 genomes]
rs9862259	1.00[ASW][hapmap];0.93[GIH][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs9875582	0.85[JPT][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7621298	CXCR6	cis	cerebellum	SCAN
rs7621298	ANO10	cis	Whole Blood	GTEx
rs7621298	SNRK	cis	cerebellum	SCAN
rs7621298	RPL14	cis	parietal	SCAN
rs7621298	PTH1R	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43373400-43393400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:43374400-43385000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:43377000-43385800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:43379000-43385400	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr3:43379600-43392800	Strong transcription	Placenta	Placenta
6	chr3:43380000-43383800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:43380000-43385200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:43380000-43387400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:43380000-43387600	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr3:43380000-43392200	Strong transcription	HepG2	liver
11	chr3:43380000-43392800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:43380200-43386200	Strong transcription	Fetal Lung	lung
13	chr3:43380200-43386800	Strong transcription	HSMM	muscle
14	chr3:43380600-43385200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:43380600-43385800	Strong transcription	Lung	lung
16	chr3:43380800-43385600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr3:43380800-43386400	Strong transcription	Brain Hippocampus Middle	brain
18	chr3:43380800-43386800	Weak transcription	Psoas Muscle	Psoas
19	chr3:43380800-43391800	Strong transcription	Fetal Stomach	stomach
20	chr3:43380800-43392600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:43380800-43392800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:43380800-43392800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:43380800-43393000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:43380800-43393200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:43381000-43383800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:43381000-43383800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:43381000-43384800	Strong transcription	Dnd41	blood
28	chr3:43381000-43385000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:43381000-43385400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:43381000-43385600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:43381000-43385600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:43381000-43386800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:43381000-43388000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:43381000-43389400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr3:43381000-43392800	Weak transcription	Fetal Brain Male	brain
36	chr3:43381000-43393800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:43381000-43396400	Weak transcription	Stomach Mucosa	stomach
38	chr3:43381200-43388800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr3:43381200-43392800	Strong transcription	Fetal Intestine Large	intestine
40	chr3:43381400-43385400	Strong transcription	Colon Smooth Muscle	Colon
41	chr3:43381400-43385600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:43381400-43385600	Strong transcription	Rectal Smooth Muscle	rectum
43	chr3:43381400-43386200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:43381400-43387600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:43381400-43392600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr3:43381400-43392800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr3:43381400-43393000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:43381600-43384400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:43381600-43386200	Strong transcription	Osteobl	bone
50	chr3:43381600-43387200	Strong transcription	Rectal Mucosa Donor 31	rectum

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