Variant report

Variant	rs2915888
Chromosome Location	chr5:151205100-151205101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:151204595..151205535-chr5:151522142..151523020,2	K562	blood:
2	chr5:151204608..151205517-chr5:151728966..151729819,3	MCF-7	breast:
3	chr5:151204602..151205567-chr5:151884635..151885219,2	K562	blood:
4	chr5:151204736..151205618-chr5:151521905..151522989,3	MCF-7	breast:
5	chr5:151204659..151205617-chr5:151544194..151544853,2	MCF-7	breast:
6	chr5:151204677..151205872-chr5:151522532..151523052,3	MCF-7	breast:
7	chr5:151150433..151152215-chr5:151203690..151206596,2	MCF-7	breast:
8	chr5:151204622..151206484-chr5:151650636..151651662,12	MCF-7	breast:
9	chr5:151199513..151202709-chr5:151203145..151205283,3	K562	blood:
10	chr5:151204730..151205623-chr5:151885147..151885688,2	MCF-7	breast:
11	chr5:151205027..151205654-chr5:151893657..151894608,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000177556	Chromatin interaction
ENSG00000145907	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10044368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10065313	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10075101	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1042877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10476776	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10476778	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1062177	0.94[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs11167557	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11950215	0.81[JPT][hapmap]
rs11954338	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12108921	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs12109022	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs12654877	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12658422	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1366238	0.80[EUR][1000 genomes]
rs1433041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1549920	0.94[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1549921	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17741826	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs17804178	0.85[ASN][1000 genomes]
rs1978710	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2016409	0.81[ASN][1000 genomes]
rs2053063	0.85[ASN][1000 genomes]
rs2347596	0.85[ASN][1000 genomes]
rs2347597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2913889	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2913892	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap]
rs2913893	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2913894	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2915816	0.88[ASN][1000 genomes]
rs2915822	0.94[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2915823	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2915824	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2915826	0.94[CHB][hapmap]
rs2915827	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2915829	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2915868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915869	0.85[ASN][1000 genomes]
rs2915870	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915871	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2915872	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915873	0.83[ASN][1000 genomes]
rs2915874	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2915876	0.94[CHB][hapmap];0.84[CHD][hapmap]
rs2915878	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs2915879	0.94[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2915880	0.94[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2915881	0.81[ASN][1000 genomes]
rs2915882	0.81[ASN][1000 genomes]
rs2915883	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2915885	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2915886	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915887	0.87[ASN][1000 genomes]
rs2915890	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915891	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915892	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915893	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915894	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964568	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2964569	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2964570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964571	0.85[ASN][1000 genomes]
rs2964572	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964573	0.82[ASN][1000 genomes]
rs2964574	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2964577	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2964578	0.81[ASN][1000 genomes]
rs2964580	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2964581	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2964582	0.81[ASN][1000 genomes]
rs2964584	0.94[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2964585	0.82[ASN][1000 genomes]
rs2964587	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2964591	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2964592	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2964610	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964611	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964612	0.85[ASN][1000 genomes]
rs2964613	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35692301	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3812003	0.81[ASW][hapmap]
rs4360031	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4362933	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4379180	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4419575	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4472253	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4510568	0.97[EUR][1000 genomes]
rs4541649	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4555782	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4571461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4594844	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4629583	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4629586	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62394144	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6579897	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs6579906	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6579908	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6579909	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6579910	0.90[EUR][1000 genomes]
rs6863833	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6863837	0.95[EUR][1000 genomes]
rs6879461	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72802204	0.85[ASN][1000 genomes]
rs7341167	0.95[EUR][1000 genomes]
rs7702751	0.94[EUR][1000 genomes]
rs7715560	0.89[EUR][1000 genomes]
rs7715874	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7719617	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7720579	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7728956	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap]
rs7733241	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7734314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7735811	0.91[EUR][1000 genomes]
rs892005	0.85[ASN][1000 genomes]
rs892006	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs973529	0.85[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2915888	C5orf46	cis	parietal	SCAN
rs2915888	SYNPO	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151164000-151207600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:151171800-151205200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:151179800-151208400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:151183600-151210600	Weak transcription	Lung	lung
5	chr5:151183800-151206000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:151183800-151208400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:151183800-151209600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:151183800-151213400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:151188200-151210400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:151190400-151210400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:151192200-151208200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:151192400-151205200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:151192400-151209800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr5:151192400-151210000	Weak transcription	Aorta	Aorta
15	chr5:151192400-151211200	Weak transcription	NHLF	lung
16	chr5:151192600-151205200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:151192600-151206000	Weak transcription	Thymus	Thymus
18	chr5:151192600-151206200	Weak transcription	Psoas Muscle	Psoas
19	chr5:151192600-151209800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:151192800-151205200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:151192800-151208400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:151192800-151209600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:151192800-151209800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:151193000-151205600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:151193000-151207600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:151193000-151210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:151193200-151210600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:151193600-151211400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:151194400-151207800	Weak transcription	Primary B cells from cord blood	blood
30	chr5:151194800-151206000	Weak transcription	Dnd41	blood
31	chr5:151194800-151206600	Weak transcription	Placenta	Placenta
32	chr5:151194800-151209000	Weak transcription	Brain Anterior Caudate	brain
33	chr5:151194800-151209600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:151194800-151210400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:151195000-151205200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:151195400-151206000	Weak transcription	K562	blood
37	chr5:151196200-151205200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:151196400-151205200	Weak transcription	Fetal Thymus	thymus
39	chr5:151196600-151205200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr5:151196600-151205600	Weak transcription	Hela-S3	cervix
41	chr5:151196600-151210400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr5:151196800-151208000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:151196800-151209400	Weak transcription	Liver	Liver
44	chr5:151196800-151211400	Weak transcription	GM12878-XiMat	blood
45	chr5:151197000-151208000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:151197000-151208200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:151197000-151211400	Weak transcription	NH-A	brain
48	chr5:151197200-151205200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr5:151197600-151205200	Weak transcription	Primary T cells from cord blood	blood
50	chr5:151198200-151210600	Weak transcription	Muscle Satellite Cultured Cells	--

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