Variant report

Variant	rs7171233
Chromosome Location	chr15:38988760-38988761
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr15:38988561-38988897	GM12878	blood:	n/a	n/a
2	SRF	chr15:38988650-38988831	GM12878	blood:	n/a	n/a
3	MAFK	chr15:38988593-38988814	K562	blood:	n/a	chr15:38988674-38988683 chr15:38988676-38988686
4	EBF1	chr15:38988652-38988972	GM12878	blood:	n/a	n/a
5	RELA	chr15:38988411-38989100	GM18951	blood:	n/a	n/a
6	RUNX3	chr15:38988172-38989078	GM12878	blood:	n/a	n/a
7	RELA	chr15:38988482-38989170	GM12891	blood:	n/a	n/a
8	RELA	chr15:38988554-38989068	GM19099	blood:	n/a	n/a
9	MAFK	chr15:38988523-38988845	IMR90	lung:	n/a	chr15:38988674-38988683 chr15:38988676-38988686
10	POLR2A	chr15:38988105-38988887	GM12892	blood:	n/a	n/a
11	RCOR1	chr15:38988557-38988861	K562	blood:	n/a	n/a
12	POLR2A	chr15:38988116-38989136	GM18951	blood:	n/a	n/a
13	POLR2A	chr15:38987602-38989220	GM19193	blood:	n/a	n/a
14	YY1	chr15:38988614-38988832	GM12878	blood:	n/a	n/a
15	EBF1	chr15:38988514-38988922	GM12878	blood:	n/a	n/a
16	JUND	chr15:38988554-38988837	K562	blood:	n/a	chr15:38988674-38988686 chr15:38988676-38988684 chr15:38988675-38988685
17	BATF	chr15:38988473-38988855	GM12878	blood:	n/a	chr15:38988673-38988683 chr15:38988672-38988683
18	RUNX3	chr15:38988468-38988960	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:38988234-38988859	GM12892	blood:	n/a	n/a
20	MYC	chr15:38988162-38989068	NB4	blood:	n/a	n/a
21	MAZ	chr15:38988638-38988787	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:38988363-38988907	GM12892	blood:	n/a	n/a
23	RELA	chr15:38987610-38989052	GM19193	blood:	n/a	n/a
24	MAX	chr15:38988389-38989119	NB4	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:38988755-38988805	K562	blood:	n/a
2	chr15:38988755-38988805	LNCaP	prostate:	n/a
3	chr15:38988755-38988805	Hepatocyte	liver:	n/a
4	chr15:38988755-38988805	HCM	heart:	n/a
5	chr15:38988755-38988805	AG04449	skin:	fetal
6	chr15:38988755-38988805	HepG2	liver:	n/a
7	chr15:38988755-38988805	HMEC	breast:	n/a
8	chr15:38988755-38988805	GM19239	blood:	n/a
9	chr15:38988755-38988805	HRCEpiC	kidney:	n/a
10	chr15:38988755-38988805	PANC-1	pancreas:	n/a
11	chr15:38988755-38988805	GM12892	blood:	n/a
12	chr15:38988755-38988805	MCF-7	breast:	n/a
13	chr15:38988755-38988805	AG09319	gingival:	n/a
14	chr15:38988755-38988805	HEK293	kidney:	embryo
15	chr15:38988755-38988805	NH-A	brain:	n/a
16	chr15:38988755-38988805	NHBE	bronchial:	n/a
17	chr15:38988755-38988805	Caco-2	colon:	n/a
18	chr15:38988755-38988805	GM12891	blood:	n/a
19	chr15:38988755-38988805	HRE	kidney:	n/a
20	chr15:38988755-38988805	AG04450	lung:	fetal
21	chr15:38988755-38988805	HNPCEpiC	eye:	n/a
22	chr15:38988755-38988805	SK-N-SH	brain:	n/a
23	chr15:38988755-38988805	BJ	skin:	n/a
24	chr15:38988755-38988805	GM12878	blood:	n/a
25	chr15:38988755-38988805	HRPEpiC	eye:	n/a
26	chr15:38988755-38988805	SK-N-SH_RA	brain:	n/a
27	chr15:38988755-38988805	HPAEpiC	pulmonary alveolar:	n/a
28	chr15:38988755-38988805	PFSK-1	brain:	n/a
29	chr15:38988755-38988805	NHDF-neo	bronchial:	n/a
30	chr15:38988755-38988805	AoSMC	blood vessel:	n/a
31	chr15:38988755-38988805	PrEC	prostate:	n/a
32	chr15:38988755-38988805	H1-hESC	embryonic stem cell:	embryo
33	chr15:38988755-38988805	IMR90	lung:	fetal
34	chr15:38988755-38988805	HCF	heart:	n/a
35	chr15:38988755-38988805	GM06990	blood:	n/a
36	chr15:38988755-38988805	HAEpiC	amniotic membrane:	n/a
37	chr15:38988755-38988805	HUVEC	blood vessel:	n/a
38	chr15:38988755-38988805	SKMC	muscle:	n/a
39	chr15:38988755-38988805	Jurkat	blood:	n/a
40	chr15:38988755-38988805	A549	lung:	n/a
41	chr15:38988755-38988805	ProgFib	skin:	n/a
42	chr15:38988755-38988805	Hela-S3	cervix:	n/a
43	chr15:38988755-38988805	MCF10A-Er-Src	breast:	n/a
44	chr15:38988755-38988805	HIPEpiC	eye:	n/a
45	chr15:38988755-38988805	HCPEpiC	choroid plexus:	n/a
46	chr15:38988755-38988805	RPTEC	kidney:	n/a
47	chr15:38988755-38988805	U87	brain:	n/a
48	chr15:38988755-38988805	T-47D	breast:	n/a
49	chr15:38988755-38988805	NT2-D1	testis:	n/a
50	chr15:38988755-38988805	NB4	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:38855702..38858314-chr15:38985984..38988881,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf53-2	chr15:38988296-38989826	l_1145_chr15:38986242-38988846_testes

No data

Variant related genes	Relation type
C15orf53	TF binding region
C15orf53	CpG island
ENSG00000172575	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12148859	0.83[ASN][1000 genomes]
rs12898460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899449	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12901215	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12903120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916379	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2132157	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2172835	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34141940	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34281605	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34356257	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35024396	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35102843	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35795311	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36094159	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71403553	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7165988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177621	0.89[EUR][1000 genomes]
rs7183893	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7171233	FLJ35695	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38978800-38990800	Weak transcription	Right Atrium	heart
2	chr15:38986200-38988800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:38986600-38992600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr15:38986600-38992600	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr15:38986800-38989200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:38986800-38992400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr15:38986800-38992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:38987000-38992000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:38987200-38988800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr15:38987200-38989200	Enhancers	GM12878-XiMat	blood
11	chr15:38987200-38989400	Enhancers	Fetal Heart	heart
12	chr15:38987200-38991800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr15:38987200-38992000	Enhancers	Primary hematopoietic stem cells	blood
14	chr15:38987200-38992400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr15:38987200-38992600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr15:38987600-38988800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:38987800-38991400	Enhancers	Dnd41	blood
18	chr15:38987800-38991800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:38987800-38991800	Enhancers	Fetal Thymus	thymus
20	chr15:38988000-38988800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:38988000-38989000	Enhancers	Placenta	Placenta
22	chr15:38988000-38989000	Enhancers	Thymus	Thymus
23	chr15:38988000-38989400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:38988000-38989400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:38988200-38989000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:38988200-38989000	Enhancers	Left Ventricle	heart
27	chr15:38988200-38989000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr15:38988200-38989000	Enhancers	HSMM	muscle
29	chr15:38988200-38989000	Enhancers	NH-A	brain
30	chr15:38988200-38989400	Enhancers	Primary T cells from cord blood	blood
31	chr15:38988200-38989400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr15:38988200-38990200	Enhancers	Duodenum Mucosa	Duodenum
33	chr15:38988400-38988800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:38988400-38988800	Enhancers	Right Ventricle	heart
35	chr15:38988400-38989000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:38988400-38989000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:38988400-38989000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:38988400-38989000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:38988400-38989000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr15:38988400-38989000	Enhancers	NHDF-Ad	bronchial
41	chr15:38988400-38989000	Enhancers	Osteobl	bone
42	chr15:38988400-38989400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:38988400-38992000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr15:38988600-38992400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:38988600-38994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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