Variant report

Variant	rs1341015
Chromosome Location	chr1:119981049-119981050
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: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	chr1:119980940-119981090	Hela-S3	cervix:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:119981031-119981081	T-47D	breast:	n/a
2	chr1:119981031-119981081	HIPEpiC	eye:	n/a
3	chr1:119981031-119981081	PANC-1	pancreas:	n/a
4	chr1:119981031-119981081	PFSK-1	brain:	n/a
5	chr1:119981031-119981081	HNPCEpiC	eye:	n/a
6	chr1:119981031-119981081	IMR90	lung:	fetal
7	chr1:119981031-119981081	ProgFib	skin:	n/a
8	chr1:119981031-119981081	LNCaP	prostate:	n/a
9	chr1:119981031-119981081	NB4	blood:	n/a
10	chr1:119981031-119981081	HRPEpiC	eye:	n/a
11	chr1:119981031-119981081	ECC-1	luminal epithelium:	n/a
12	chr1:119981031-119981081	NH-A	brain:	n/a
13	chr1:119981031-119981081	GM19239	blood:	n/a
14	chr1:119981031-119981081	K562	blood:	n/a
15	chr1:119981031-119981081	A549	lung:	n/a
16	chr1:119981031-119981081	SAEC	small airway:	n/a
17	chr1:119981031-119981081	SK-N-MC	brain:	n/a
18	chr1:119981031-119981081	U87	brain:	n/a
19	chr1:119981031-119981081	RPTEC	kidney:	n/a
20	chr1:119981031-119981081	PrEC	prostate:	n/a
21	chr1:119981031-119981081	CMK	blood:	n/a
22	chr1:119981031-119981081	GM12892	blood:	n/a
23	chr1:119981031-119981081	AoSMC	blood vessel:	n/a
24	chr1:119981031-119981081	Hepatocyte	liver:	n/a
25	chr1:119981031-119981081	AG10803	skin:	n/a
26	chr1:119981031-119981081	SK-N-SH_RA	brain:	n/a
27	chr1:119981031-119981081	Hela-S3	cervix:	n/a
28	chr1:119981031-119981081	HRE	kidney:	n/a
29	chr1:119981031-119981081	HPAEpiC	pulmonary alveolar:	n/a
30	chr1:119981031-119981081	SK-N-SH	brain:	n/a
31	chr1:119981031-119981081	NHBE	bronchial:	n/a
32	chr1:119981031-119981081	H1-hESC	embryonic stem cell:	embryo
33	chr1:119981031-119981081	AG04449	skin:	fetal
34	chr1:119981031-119981081	ovcar-3	ovarian:	n/a
35	chr1:119981031-119981081	AG09309	skin:	n/a
36	chr1:119981031-119981081	GM06990	blood:	n/a
37	chr1:119981031-119981081	Jurkat	blood:	n/a
38	chr1:119981031-119981081	GM12891	blood:	n/a
39	chr1:119981031-119981081	HAEpiC	amniotic membrane:	n/a
40	chr1:119981031-119981081	HepG2	liver:	n/a
41	chr1:119981031-119981081	GM12878	blood:	n/a
42	chr1:119981031-119981081	HEEpiC	esophagus:	n/a
43	chr1:119981031-119981081	AG09319	gingival:	n/a
44	chr1:119981031-119981081	NHDF-neo	bronchial:	n/a
45	chr1:119981031-119981081	NT2-D1	testis:	n/a
46	chr1:119981031-119981081	SKMC	muscle:	n/a
47	chr1:119981031-119981081	BE2_C	brain:	n/a
48	chr1:119981031-119981081	HUVEC	blood vessel:	n/a
49	chr1:119981031-119981081	MCF10A-Er-Src	breast:	n/a
50	chr1:119981031-119981081	Caco-2	colon:	n/a

No data

Variant related genes	Relation type
HSD3BP2	TF binding region
ENSG00000232780	TF binding region
ENSG00000232780	CpG island
HSD3BP2	CpG island

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10489811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494225	1.00[CHB][hapmap]
rs10923825	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11579951	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582671	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585256	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801567	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802093	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11802681	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802702	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805965	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361530	0.83[CEU][hapmap]
rs1417607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1417608	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417609	0.84[CEU][hapmap]
rs1417610	0.85[CEU][hapmap]
rs17023577	0.91[CEU][hapmap]
rs17023625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856886	1.00[CHB][hapmap]
rs2185557	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275608	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs3753260	1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[MEX][hapmap]
rs3753266	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs5003333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57778712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59922917	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683756	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs72691196	0.94[EUR][1000 genomes]
rs7514283	1.00[CHB][hapmap]
rs7529983	1.00[CHB][hapmap]
rs7530593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550369	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	esv2763647	chr1:119929442-120154798	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv946176	chr1:119960027-119989077	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv3431786	chr1:119977797-120005821	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1341015	CD58	cis	cerebellum	SCAN
rs1341015	NHLH2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119980600-119986800	Enhancers	Fetal Intestine Large	intestine
2	chr1:119980800-119982000	Enhancers	Fetal Intestine Small	intestine
3	chr1:119981000-119981600	Weak transcription	Adipose Nuclei	Adipose

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