Variant report

Variant	rs10489279
Chromosome Location	chr1:172498216-172498217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr1:172498060-172498684	HepG2	liver:	n/a	chr1:172498134-172498150

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:172498191-172498241	Hepatocyte	liver:	n/a
2	chr1:172498191-172498241	NH-A	brain:	n/a
3	chr1:172498191-172498241	AG10803	skin:	n/a
4	chr1:172498191-172498241	SK-N-MC	brain:	n/a
5	chr1:172498191-172498241	T-47D	breast:	n/a
6	chr1:172498191-172498241	ECC-1	luminal epithelium:	n/a
7	chr1:172498191-172498241	ovcar-3	ovarian:	n/a
8	chr1:172498191-172498241	BE2_C	brain:	n/a
9	chr1:172498191-172498241	AoSMC	blood vessel:	n/a
10	chr1:172498191-172498241	U87	brain:	n/a
11	chr1:172498191-172498241	SAEC	small airway:	n/a
12	chr1:172498191-172498241	HRPEpiC	eye:	n/a
13	chr1:172498191-172498241	HMEC	breast:	n/a
14	chr1:172498191-172498241	PrEC	prostate:	n/a
15	chr1:172498191-172498241	HCM	heart:	n/a
16	chr1:172498191-172498241	HIPEpiC	eye:	n/a
17	chr1:172498191-172498241	SKMC	muscle:	n/a
18	chr1:172498191-172498241	HCPEpiC	choroid plexus:	n/a
19	chr1:172498191-172498241	AG09309	skin:	n/a
20	chr1:172498191-172498241	AG04450	lung:	fetal
21	chr1:172498191-172498241	IMR90	lung:	fetal
22	chr1:172498191-172498241	HRE	kidney:	n/a
23	chr1:172498191-172498241	MCF-7	breast:	n/a
24	chr1:172498191-172498241	HL-60	blood:	n/a
25	chr1:172498191-172498241	HEK293	kidney:	embryo
26	chr1:172498191-172498241	HNPCEpiC	eye:	n/a
27	chr1:172498191-172498241	CMK	blood:	n/a
28	chr1:172498191-172498241	A549	lung:	n/a
29	chr1:172498191-172498241	ProgFib	skin:	n/a
30	chr1:172498191-172498241	Jurkat	blood:	n/a
31	chr1:172498191-172498241	GM12892	blood:	n/a
32	chr1:172498191-172498241	AG09319	gingival:	n/a
33	chr1:172498191-172498241	MCF10A-Er-Src	breast:	n/a
34	chr1:172498191-172498241	NT2-D1	testis:	n/a
35	chr1:172498191-172498241	SK-N-SH	brain:	n/a
36	chr1:172498191-172498241	HepG2	liver:	n/a
37	chr1:172498191-172498241	HAEpiC	amniotic membrane:	n/a
38	chr1:172498191-172498241	Hela-S3	cervix:	n/a
39	chr1:172498191-172498241	NHDF-neo	bronchial:	n/a
40	chr1:172498191-172498241	K562	blood:	n/a
41	chr1:172498191-172498241	H1-hESC	embryonic stem cell:	embryo
42	chr1:172498191-172498241	AG04449	skin:	fetal
43	chr1:172498191-172498241	RPTEC	kidney:	n/a
44	chr1:172498191-172498241	HEEpiC	esophagus:	n/a
45	chr1:172498191-172498241	HPAEpiC	pulmonary alveolar:	n/a
46	chr1:172498191-172498241	HRCEpiC	kidney:	n/a
47	chr1:172498191-172498241	HUVEC	blood vessel:	n/a
48	chr1:172498191-172498241	LNCaP	prostate:	n/a
49	chr1:172498191-172498241	BJ	skin:	n/a
50	chr1:172498191-172498241	NB4	blood:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:172411084..172422561-chr1:172496524..172504623,44	MCF-7	breast:
2	chr1:172486127..172488704-chr1:172497575..172501072,3	MCF-7	breast:
3	chr1:172439490..172443248-chr1:172495023..172498932,4	MCF-7	breast:
4	chr1:172440495..172444630-chr1:172497465..172500697,4	MCF-7	breast:
5	chr1:172469701..172471621-chr1:172497308..172500120,2	K562	blood:
6	chr1:172471627..172474558-chr1:172496205..172498413,2	MCF-7	breast:
7	chr1:172412087..172424934-chr1:172497120..172505334,59	MCF-7	breast:

No data

Variant related genes	Relation type
SUCO	TF binding region
SUCO	CpG island
ENSG00000180999	Chromatin interaction
ENSG00000135845	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10489278	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10911822	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs10911823	0.80[ASN][1000 genomes]
rs12117531	0.80[ASN][1000 genomes]
rs12724887	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12727056	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12729335	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12729948	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12730136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731039	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12731130	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12737154	0.83[EUR][1000 genomes]
rs12739997	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12740436	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12743641	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12749864	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12750740	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12752056	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12752646	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12753093	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12754650	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12756519	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12758548	0.80[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12760161	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16844658	0.85[LWK][hapmap]
rs17370159	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1984403	0.91[CEU][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2227189	0.81[ASN][1000 genomes]
rs2516064	0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3213552	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34134854	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35702642	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35780299	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754424	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6672570	0.81[LWK][hapmap]
rs68164208	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7517917	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549441	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10489279	CD247	cis	parietal	SCAN
rs10489279	SNORD47	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172487800-172499000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:172492600-172499000	Weak transcription	K562	blood
3	chr1:172495800-172500400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:172497000-172498400	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr1:172498200-172500600	Enhancers	HepG2	liver
6	chr1:172498200-172501200	Enhancers	Placenta Amnion	Placenta Amnion

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