Variant report

Variant	rs9631455
Chromosome Location	chr3:120174450-120174451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:120174428-120174478	PrEC	prostate:	n/a
2	chr3:120174428-120174478	AoSMC	blood vessel:	n/a
3	chr3:120174428-120174478	NB4	blood:	n/a
4	chr3:120174428-120174478	BE2_C	brain:	n/a
5	chr3:120174428-120174478	K562	blood:	n/a
6	chr3:120174428-120174478	SK-N-SH	brain:	n/a
7	chr3:120174428-120174478	HUVEC	blood vessel:	n/a
8	chr3:120174428-120174478	HL-60	blood:	n/a
9	chr3:120174428-120174478	H1-hESC	embryonic stem cell:	embryo
10	chr3:120174428-120174478	HNPCEpiC	eye:	n/a
11	chr3:120174428-120174478	GM12878	blood:	n/a
12	chr3:120174428-120174478	LNCaP	prostate:	n/a
13	chr3:120174428-120174478	IMR90	lung:	fetal
14	chr3:120174428-120174478	BJ	skin:	n/a
15	chr3:120174428-120174478	HAEpiC	amniotic membrane:	n/a
16	chr3:120174428-120174478	ECC-1	luminal epithelium:	n/a
17	chr3:120174428-120174478	PFSK-1	brain:	n/a
18	chr3:120174428-120174478	HepG2	liver:	n/a
19	chr3:120174428-120174478	NH-A	brain:	n/a
20	chr3:120174428-120174478	ProgFib	skin:	n/a
21	chr3:120174428-120174478	HEEpiC	esophagus:	n/a
22	chr3:120174428-120174478	NT2-D1	testis:	n/a
23	chr3:120174428-120174478	HRCEpiC	kidney:	n/a
24	chr3:120174428-120174478	A549	lung:	n/a
25	chr3:120174428-120174478	SK-N-MC	brain:	n/a
26	chr3:120174428-120174478	HCPEpiC	choroid plexus:	n/a
27	chr3:120174428-120174478	ovcar-3	ovarian:	n/a
28	chr3:120174428-120174478	Jurkat	blood:	n/a
29	chr3:120174428-120174478	AG09319	gingival:	n/a
30	chr3:120174428-120174478	SKMC	muscle:	n/a
31	chr3:120174428-120174478	AG09309	skin:	n/a
32	chr3:120174428-120174478	GM12891	blood:	n/a
33	chr3:120174428-120174478	HMEC	breast:	n/a
34	chr3:120174428-120174478	HPAEpiC	pulmonary alveolar:	n/a
35	chr3:120174428-120174478	GM12892	blood:	n/a
36	chr3:120174428-120174478	Hela-S3	cervix:	n/a
37	chr3:120174428-120174478	HEK293	kidney:	embryo
38	chr3:120174428-120174478	HCF	heart:	n/a
39	chr3:120174428-120174478	Caco-2	colon:	n/a
40	chr3:120174428-120174478	T-47D	breast:	n/a
41	chr3:120174428-120174478	AG04450	lung:	fetal
42	chr3:120174428-120174478	PANC-1	pancreas:	n/a
43	chr3:120174428-120174478	AG10803	skin:	n/a
44	chr3:120174428-120174478	CMK	blood:	n/a
45	chr3:120174428-120174478	HRPEpiC	eye:	n/a
46	chr3:120174428-120174478	HCM	heart:	n/a
47	chr3:120174428-120174478	SK-N-SH_RA	brain:	n/a
48	chr3:120174428-120174478	SAEC	small airway:	n/a
49	chr3:120174428-120174478	NHDF-neo	bronchial:	n/a
50	chr3:120174428-120174478	GM06990	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120169575..120171438-chr3:120172846..120174747,2	MCF-7	breast:

No data

Variant related genes	Relation type
FSTL1	CpG island
ENSG00000163430	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1123897	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1123898	0.96[ASN][1000 genomes]
rs1147706	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1147709	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1147710	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1147717	0.81[ASN][1000 genomes]
rs1147720	0.88[CHB][hapmap]
rs1259311	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];0.98[ASN][1000 genomes]
rs1259318	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs1259329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259331	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259332	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259333	0.85[JPT][hapmap]
rs1259334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259335	0.83[JPT][hapmap]
rs1259336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1259338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259339	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1259457	0.81[ASN][1000 genomes]
rs1259471	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1259472	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1259473	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1267675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1270209	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520881	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716835	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1716837	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1733296	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[EUR][1000 genomes]
rs1733298	0.93[EUR][1000 genomes]
rs1733299	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1733301	0.93[EUR][1000 genomes]
rs1733303	0.93[EUR][1000 genomes]
rs1733304	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1733306	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1733307	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1733319	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1982186	0.81[ASN][1000 genomes]
rs2252084	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs2700263	0.90[ASN][1000 genomes]
rs2702155	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5000757	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6768839	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs735138	0.83[EUR][1000 genomes]
rs874477	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs874478	0.95[EUR][1000 genomes]
rs874479	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs874480	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9631455	NR1I2	cis	cerebellum	SCAN
rs9631455	FSTL1	cis	parietal	SCAN
rs9631455	FSTL1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120170400-120190800	Weak transcription	Aorta	Aorta
2	chr3:120170600-120178000	Weak transcription	Left Ventricle	heart
3	chr3:120170600-120178800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:120170800-120178200	Weak transcription	Right Atrium	heart
5	chr3:120171000-120179600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:120171400-120179400	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:120171800-120180600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:120173600-120177200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:120173600-120179200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:120174400-120174600	Enhancers	Rectal Mucosa Donor 31	rectum

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