Variant report

Variant	rs1042877
Chromosome Location	chr5:151190104-151190105
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:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:151188774..151191412-chr5:151194623..151196170,2	K562	blood:
2	chr5:151178691..151181184-chr5:151187430..151191088,3	MCF-7	breast:
3	chr5:151185556..151188449-chr5:151190002..151191608,2	K562	blood:
4	chr5:151182482..151184188-chr5:151187460..151190410,2	K562	blood:
5	chr5:151187727..151190310-chr5:151192667..151196018,4	K562	blood:
6	chr5:151182688..151184875-chr5:151188574..151190410,2	K562	blood:
7	chr5:151151269..151153817-chr5:151189460..151191892,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC36A1-5	chr5:151186316-151190911	NONHSAT104639
2	lnc-SLC36A1-5	chr5:151187002-151190915	NONHSAT104640

No data

Variant related genes	Relation type
ENSG00000145907	Chromatin interaction
ENSG00000177556	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10044368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10065313	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10075101	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10476776	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10476778	0.96[EUR][1000 genomes]
rs1062177	0.94[CHB][hapmap];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs11167557	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11954338	0.97[EUR][1000 genomes]
rs12108921	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs12109022	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12654877	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658422	0.95[EUR][1000 genomes]
rs1433041	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549920	0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs1549921	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17741826	0.94[CHB][hapmap]
rs17804178	0.85[ASN][1000 genomes]
rs1978710	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[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];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2913889	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs2913892	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2913893	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2913894	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2915816	0.87[ASN][1000 genomes]
rs2915821	0.84[ASN][1000 genomes]
rs2915822	0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs2915823	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915824	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915826	0.94[CHB][hapmap]
rs2915827	0.94[CHB][hapmap]
rs2915829	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915869	0.85[ASN][1000 genomes]
rs2915870	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915871	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915872	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915873	0.82[ASN][1000 genomes]
rs2915874	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915876	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs2915878	0.94[CHB][hapmap]
rs2915879	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs2915880	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs2915881	0.81[ASN][1000 genomes]
rs2915882	0.81[ASN][1000 genomes]
rs2915883	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915885	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2915886	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915887	0.82[ASN][1000 genomes]
rs2915888	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]
rs2915890	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915891	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915892	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915893	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915894	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964568	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964569	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964571	0.85[ASN][1000 genomes]
rs2964572	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964573	0.82[ASN][1000 genomes]
rs2964574	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs2964577	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964578	0.81[ASN][1000 genomes]
rs2964580	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964581	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964582	0.81[ASN][1000 genomes]
rs2964584	0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs2964585	0.82[ASN][1000 genomes]
rs2964587	0.94[CHB][hapmap]
rs2964591	0.94[CHB][hapmap]
rs2964592	0.94[CHB][hapmap]
rs2964610	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964611	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964612	0.83[ASN][1000 genomes]
rs2964613	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35692301	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4075273	0.81[AFR][1000 genomes]
rs4076138	0.81[AFR][1000 genomes]
rs4360031	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4362933	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4379180	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4419575	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4472253	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4510568	0.97[EUR][1000 genomes]
rs4541649	0.96[EUR][1000 genomes]
rs4555782	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4571461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4594844	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4629583	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4629586	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62394144	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6579897	0.94[CHB][hapmap]
rs6579906	0.96[EUR][1000 genomes]
rs6579908	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6579909	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6579910	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6863833	0.95[EUR][1000 genomes]
rs6863837	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6879461	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896518	0.81[AFR][1000 genomes]
rs72802204	0.85[ASN][1000 genomes]
rs7341167	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7702751	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7711609	0.81[AFR][1000 genomes]
rs7711771	0.81[AFR][1000 genomes]
rs7715560	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7715874	0.92[EUR][1000 genomes]
rs7719617	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7720579	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725327	0.81[AFR][1000 genomes]
rs7728956	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7733241	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7734314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735811	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs892005	0.85[ASN][1000 genomes]
rs892006	0.94[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs973529	0.85[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1042877	SYNPO	cis	parietal	SCAN
rs1042877	C5orf46	cis	parietal	SCAN
rs1042877	LOC729421	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151164000-151196600	Strong transcription	Hela-S3	cervix
2	chr5:151164000-151207600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:151164400-151194800	Strong transcription	Dnd41	blood
4	chr5:151164600-151197000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:151164800-151196600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:151164800-151196800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:151165200-151197200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:151165600-151191600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:151165600-151197200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:151165800-151192800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr5:151165800-151193000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr5:151165800-151194800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr5:151165800-151195000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:151165800-151196200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:151165800-151196800	Strong transcription	GM12878-XiMat	blood
16	chr5:151165800-151197000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:151166000-151192800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:151166000-151194800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:151166000-151196400	Strong transcription	Fetal Thymus	thymus
20	chr5:151166000-151196600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr5:151166000-151196800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:151166000-151197000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:151166200-151192800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr5:151166200-151196800	Strong transcription	Liver	Liver
25	chr5:151166400-151192400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:151166600-151194800	Strong transcription	Fetal Intestine Large	intestine
27	chr5:151167200-151191600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:151167200-151195000	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr5:151171800-151205200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr5:151178000-151195200	Weak transcription	Fetal Brain Male	brain
31	chr5:151179000-151198600	Strong transcription	A549	lung
32	chr5:151179400-151192600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr5:151179600-151196400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:151179800-151208400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:151183000-151199600	Weak transcription	Small Intestine	intestine
36	chr5:151183200-151195400	Strong transcription	K562	blood
37	chr5:151183600-151192000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr5:151183600-151210600	Weak transcription	Lung	lung
39	chr5:151183800-151191200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr5:151183800-151191600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr5:151183800-151191600	Weak transcription	Aorta	Aorta
42	chr5:151183800-151193400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:151183800-151194400	Weak transcription	Colonic Mucosa	Colon
44	chr5:151183800-151194800	Weak transcription	Spleen	Spleen
45	chr5:151183800-151196200	Weak transcription	Esophagus	oesophagus
46	chr5:151183800-151196400	Strong transcription	HUVEC	blood vessel
47	chr5:151183800-151199600	Weak transcription	Fetal Intestine Small	intestine
48	chr5:151183800-151200200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr5:151183800-151203000	Weak transcription	Gastric	stomach
50	chr5:151183800-151204400	Weak transcription	Pancreas	Pancrea

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