Variant report

Variant	rs6658559
Chromosome Location	chr1:84467412-84467413
allele	A/G
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:0)
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	CTCF	chr1:84467360-84467510	GM12872	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:84467405-84467455	HEEpiC	esophagus:	n/a
2	chr1:84467405-84467455	Jurkat	blood:	n/a
3	chr1:84467405-84467455	IMR90	lung:	fetal
4	chr1:84467405-84467455	AG04450	lung:	fetal
5	chr1:84467405-84467455	HCT-116	colon:	n/a
6	chr1:84467405-84467455	ovcar-3	ovarian:	n/a
7	chr1:84467405-84467455	U87	brain:	n/a
8	chr1:84467405-84467455	BE2_C	brain:	n/a
9	chr1:84467405-84467455	HRCEpiC	kidney:	n/a
10	chr1:84467405-84467455	CMK	blood:	n/a
11	chr1:84467405-84467455	NHDF-neo	bronchial:	n/a
12	chr1:84467405-84467455	HPAEpiC	pulmonary alveolar:	n/a
13	chr1:84467405-84467455	AG10803	skin:	n/a
14	chr1:84467405-84467455	SKMC	muscle:	n/a
15	chr1:84467405-84467455	GM12878	blood:	n/a
16	chr1:84467405-84467455	GM06990	blood:	n/a
17	chr1:84467405-84467455	HNPCEpiC	eye:	n/a
18	chr1:84467405-84467455	HepG2	liver:	n/a
19	chr1:84467405-84467455	ProgFib	skin:	n/a
20	chr1:84467405-84467455	HCPEpiC	choroid plexus:	n/a
21	chr1:84467405-84467455	HCM	heart:	n/a
22	chr1:84467405-84467455	NHBE	bronchial:	n/a
23	chr1:84467405-84467455	AG09319	gingival:	n/a
24	chr1:84467405-84467455	HAEpiC	amniotic membrane:	n/a
25	chr1:84467405-84467455	NH-A	brain:	n/a
26	chr1:84467405-84467455	GM19239	blood:	n/a
27	chr1:84467405-84467455	Caco-2	colon:	n/a
28	chr1:84467405-84467455	ECC-1	luminal epithelium:	n/a
29	chr1:84467405-84467455	Hela-S3	cervix:	n/a
30	chr1:84467405-84467455	HRPEpiC	eye:	n/a
31	chr1:84467405-84467455	PrEC	prostate:	n/a
32	chr1:84467405-84467455	H1-hESC	embryonic stem cell:	embryo
33	chr1:84467405-84467455	SK-N-SH	brain:	n/a
34	chr1:84467405-84467455	LNCaP	prostate:	n/a
35	chr1:84467405-84467455	K562	blood:	n/a
36	chr1:84467405-84467455	AG09309	skin:	n/a
37	chr1:84467405-84467455	PFSK-1	brain:	n/a
38	chr1:84467405-84467455	HIPEpiC	eye:	n/a
39	chr1:84467405-84467455	AG04449	skin:	fetal
40	chr1:84467405-84467455	NT2-D1	testis:	n/a
41	chr1:84467405-84467455	SK-N-SH_RA	brain:	n/a
42	chr1:84467405-84467455	GM12891	blood:	n/a
43	chr1:84467405-84467455	BJ	skin:	n/a
44	chr1:84467405-84467455	HUVEC	blood vessel:	n/a
45	chr1:84467405-84467455	SK-N-MC	brain:	n/a
46	chr1:84467405-84467455	MCF10A-Er-Src	breast:	n/a
47	chr1:84467405-84467455	HMEC	breast:	n/a
48	chr1:84467405-84467455	NB4	blood:	n/a
49	chr1:84467405-84467455	HCF	heart:	n/a
50	chr1:84467405-84467455	HL-60	blood:	n/a

No data

Variant related genes	Relation type
TTLL7	TF binding region
TTLL7	CpG island

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10127737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10465746	0.93[ASN][1000 genomes]
rs10493741	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10493744	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10874423	0.90[ASN][1000 genomes]
rs10874424	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[ASN][1000 genomes]
rs11163861	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11163862	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11163865	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs11163866	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs11163867	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs11163868	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11163872	0.85[ASN][1000 genomes]
rs11163874	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11163875	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11163876	0.94[ASN][1000 genomes]
rs11163877	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[ASN][1000 genomes]
rs11163878	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11163879	0.97[ASN][1000 genomes]
rs11163884	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163885	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163886	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163887	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11807807	0.94[ASN][1000 genomes]
rs12070578	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12118434	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12119275	0.96[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12121175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127266	0.88[ASN][1000 genomes]
rs12133778	0.88[ASN][1000 genomes]
rs12135028	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12139191	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[ASN][1000 genomes]
rs12140068	0.93[ASN][1000 genomes]
rs12141272	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[ASN][1000 genomes]
rs12145258	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[ASN][1000 genomes]
rs12145516	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146038	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12184292	0.84[ASN][1000 genomes]
rs12401314	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12402130	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12403631	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12406984	0.92[ASN][1000 genomes]
rs12407641	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12410398	0.96[ASN][1000 genomes]
rs12410617	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12723239	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12730621	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[ASN][1000 genomes]
rs12732697	0.83[ASN][1000 genomes]
rs12738214	0.84[ASN][1000 genomes]
rs12748268	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12749350	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[ASN][1000 genomes]
rs12757632	0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs12758441	0.83[ASN][1000 genomes]
rs12759527	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1324484	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1324486	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.92[ASN][1000 genomes]
rs1359331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1475263	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1536165	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1536166	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1570690	0.90[ASN][1000 genomes]
rs1570691	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1602999	0.90[EUR][1000 genomes]
rs17099118	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17475760	0.95[ASN][1000 genomes]
rs17534614	0.91[ASN][1000 genomes]
rs1871924	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs1871925	0.97[ASN][1000 genomes]
rs1886769	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886770	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1925710	0.95[ASN][1000 genomes]
rs1952065	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[YRI][hapmap];0.96[ASN][1000 genomes]
rs1952066	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[ASN][1000 genomes]
rs2024591	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2147392	0.91[ASN][1000 genomes]
rs2147950	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2224990	0.98[ASN][1000 genomes]
rs2389616	0.96[ASN][1000 genomes]
rs2389617	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2389647	0.91[ASN][1000 genomes]
rs2389648	0.92[ASN][1000 genomes]
rs2389649	0.91[ASN][1000 genomes]
rs2477201	0.85[JPT][hapmap]
rs28445286	0.96[ASN][1000 genomes]
rs28567085	0.98[ASN][1000 genomes]
rs28726372	0.81[ASN][1000 genomes]
rs34155960	0.96[ASN][1000 genomes]
rs34274953	0.87[ASN][1000 genomes]
rs34636124	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35485748	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35946036	0.98[ASN][1000 genomes]
rs35969331	0.98[ASN][1000 genomes]
rs4258241	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4907186	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4907188	0.84[ASN][1000 genomes]
rs4907189	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4907190	0.96[ASN][1000 genomes]
rs4907191	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs558567	0.85[JPT][hapmap]
rs575633	0.85[JPT][hapmap]
rs598531	0.85[JPT][hapmap]
rs639666	0.85[JPT][hapmap]
rs663136	0.85[JPT][hapmap]
rs6667468	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6670658	0.98[ASN][1000 genomes]
rs6685344	0.86[ASN][1000 genomes]
rs6687372	0.98[ASN][1000 genomes]
rs6692233	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6694752	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6699501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[ASN][1000 genomes]
rs670284	0.85[JPT][hapmap]
rs6703382	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6703493	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs685472	0.85[JPT][hapmap]
rs686839	0.85[JPT][hapmap]
rs7531537	0.96[ASN][1000 genomes]
rs7550413	0.80[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7551787	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs882897	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.99[ASN][1000 genomes]
rs936661	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs942848	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs942849	0.98[ASN][1000 genomes]
rs9660265	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs980417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs980418	0.89[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6658559	LPHN2	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84465800-84467800	Weak transcription	HUVEC	blood vessel
2	chr1:84465800-84467800	Weak transcription	NHEK	skin
3	chr1:84465800-84468000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:84465800-84468200	Weak transcription	HMEC	breast
5	chr1:84466400-84467600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr1:84466400-84468200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:84467000-84467600	Enhancers	Aorta	Aorta
8	chr1:84467000-84467600	Enhancers	Brain Angular Gyrus	brain
9	chr1:84467000-84467600	Enhancers	Brain Hippocampus Middle	brain
10	chr1:84467000-84467600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:84467000-84467600	Enhancers	Brain Substantia Nigra	brain
12	chr1:84467000-84467800	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:84467200-84467600	Enhancers	Brain Anterior Caudate	brain
14	chr1:84467200-84467600	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links