Variant report

Variant	rs17214746
Chromosome Location	chr3:150351268-150351269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150349271..150351957-chr3:150449849..150451652,2	K562	blood:
2	chr3:150336339..150339274-chr3:150349708..150351395,2	K562	blood:
3	chr3:150344657..150347159-chr3:150348662..150351460,3	K562	blood:
4	chr3:150340005..150343317-chr3:150348325..150351775,4	K562	blood:

Variant related genes	Relation type
ENSG00000198843	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11548666	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11922033	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11927175	0.83[EUR][1000 genomes]
rs11927998	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12107730	0.83[EUR][1000 genomes]
rs17214539	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs17440940	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2030530	0.83[EUR][1000 genomes]
rs2293150	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2293151	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs55707430	0.83[EUR][1000 genomes]
rs55723846	0.81[EUR][1000 genomes]
rs56208302	0.83[EUR][1000 genomes]
rs59885545	0.83[EUR][1000 genomes]
rs60142519	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61667461	0.83[EUR][1000 genomes]
rs73001362	0.83[EUR][1000 genomes]
rs73001363	0.82[EUR][1000 genomes]
rs73001365	0.83[EUR][1000 genomes]
rs73003042	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17214746	SELT	cis	parietal	SCAN
rs17214746	UBQLN4	cis	parietal	SCAN
rs17214746	SELT	cis	cerebellum	SCAN
rs17214746	TM4SF4	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150322400-150353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:150326000-150352800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:150330000-150356600	Weak transcription	Gastric	stomach
4	chr3:150330200-150353000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:150334800-150352800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:150339800-150353000	Weak transcription	HepG2	liver
7	chr3:150342600-150353200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:150344200-150351400	Weak transcription	Pancreas	Pancrea
9	chr3:150344400-150352800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:150344400-150353800	Weak transcription	Brain Angular Gyrus	brain
11	chr3:150344600-150352200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:150344600-150353200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:150344800-150353000	Weak transcription	Psoas Muscle	Psoas
14	chr3:150344800-150353200	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:150345000-150352800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:150345000-150353000	Weak transcription	Small Intestine	intestine
17	chr3:150345000-150354000	Weak transcription	Esophagus	oesophagus
18	chr3:150345200-150353000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:150345600-150351400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:150345600-150352600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:150345600-150352800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:150345600-150352800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:150345600-150353000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:150345600-150353000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:150345600-150353200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:150345600-150353200	Weak transcription	NHDF-Ad	bronchial
27	chr3:150345800-150352000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:150345800-150352200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:150345800-150352800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:150345800-150352800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:150345800-150352800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:150345800-150353200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:150345800-150353200	Weak transcription	Fetal Kidney	kidney
34	chr3:150345800-150359400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:150346000-150353000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:150346800-150352800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:150347000-150352000	Weak transcription	HSMM	muscle
38	chr3:150347000-150352800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:150347000-150353200	Weak transcription	Primary B cells from cord blood	blood
40	chr3:150347200-150352800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:150347600-150352800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:150348600-150352800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:150348600-150352800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:150348800-150352000	Weak transcription	Osteobl	bone
45	chr3:150348800-150354200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:150349000-150352800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:150349000-150352800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:150349000-150352800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:150349000-150352800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:150349000-150352800	Weak transcription	Thymus	Thymus

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