Variant report

Variant	rs4779670
Chromosome Location	chr15:30117746-30117747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF1	chr15:30117551-30117790	K562	blood:	n/a	n/a
2	GATA3	chr15:30117338-30118093	SH-SY5Y	brain:	n/a	n/a
3	TBL1XR1	chr15:30117285-30118090	K562	blood:	n/a	n/a
4	GATA2	chr15:30117215-30117920	HUVEC	blood vessel:	n/a	n/a
5	MAFK	chr15:30117517-30117958	K562	blood:	n/a	n/a
6	RCOR1	chr15:30117289-30117938	K562	blood:	n/a	n/a
7	GATA3	chr15:30117311-30117953	SK-N-SH	brain:	n/a	n/a
8	CCNT2	chr15:30117280-30117748	K562	blood:	n/a	n/a
9	ZMIZ1	chr15:30117602-30117787	K562	blood:	n/a	n/a
10	TEAD4	chr15:30117403-30117855	K562	blood:	n/a	n/a
11	IRF1	chr15:30117740-30118047	K562	blood:	n/a	n/a
12	POLR2A	chr15:30117485-30117779	SK-N-MC	brain:	n/a	n/a
13	RCOR1	chr15:30117473-30117859	K562	blood:	n/a	n/a
14	GATA3	chr15:30117247-30117968	SK-N-SH	brain:	n/a	n/a
15	TEAD4	chr15:30117261-30117869	SK-N-SH	brain:	n/a	n/a
16	GABPA	chr15:30117298-30117883	HL-60	blood:	n/a	n/a
17	POLR2A	chr15:30117334-30117912	HL-60	blood:	n/a	n/a
18	RUNX3	chr15:30117353-30117858	GM12878	blood:	n/a	chr15:30117559-30117568 chr15:30117559-30117568 chr15:30117633-30117642 chr15:30117633-30117642
19	EP300	chr15:30117405-30118037	K562	blood:	n/a	chr15:30117886-30117895
20	RUNX3	chr15:30117274-30117880	GM12878	blood:	n/a	chr15:30117559-30117568 chr15:30117559-30117568 chr15:30117633-30117642 chr15:30117633-30117642
21	EBF1	chr15:30117544-30117816	GM12878	blood:	n/a	n/a
22	ZNF384	chr15:30117479-30117775	K562	blood:	n/a	n/a
23	POLR2A	chr15:30117650-30117894	MCF10A-Er-Src	breast:	n/a	n/a
24	CUX1	chr15:30117399-30117807	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:30117277..30119104-chr15:30123293..30126134,3	MCF-7	breast:
2	chr15:30113090..30115260-chr15:30117657..30120039,3	MCF-7	breast:
3	chr15:30116855..30119130-chr15:30151022..30153262,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GOLGA8J-2	chr15:30117587-30117856	XLOC_011197

Variant related genes	Relation type
TJP1	TF binding region
ENSG00000104067	Chromatin interaction
ENSG00000259523	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10152681	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10775231	0.95[CEU][hapmap]
rs11073218	0.90[JPT][hapmap]
rs12438925	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12440211	0.81[EUR][1000 genomes]
rs12440708	0.84[EUR][1000 genomes]
rs12441554	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1383315	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1480503	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1552077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1585900	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1871678	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2032	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2229518	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2337167	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs260531	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs260532	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs260533	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs260534	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs260535	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs260538	0.82[ASN][1000 genomes]
rs28675809	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2878893	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2878905	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4073316	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4362339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4780258	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4780259	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4780260	0.94[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4780263	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495914	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495927	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495935	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495945	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs7166786	0.82[EUR][1000 genomes]
rs7168919	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7170406	0.94[CEU][hapmap]
rs7171815	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176476	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176594	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7180387	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs767514	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs785445	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8023974	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027827	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	esv1845759	chr15:30097078-30142373	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30115400-30119400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:30115400-30121000	Weak transcription	Lung	lung
3	chr15:30115600-30118600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr15:30115600-30118800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:30115600-30119000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:30115600-30119000	Weak transcription	Brain Angular Gyrus	brain
7	chr15:30115600-30119000	Weak transcription	Left Ventricle	heart
8	chr15:30115600-30119000	Weak transcription	Right Atrium	heart
9	chr15:30115600-30119200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:30115600-30119600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:30115600-30124400	Weak transcription	Spleen	Spleen
12	chr15:30115600-30127200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:30115600-30132800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:30115600-30136000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:30115800-30118800	Weak transcription	Brain Hippocampus Middle	brain
16	chr15:30115800-30119000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:30115800-30119200	Weak transcription	Brain Anterior Caudate	brain
18	chr15:30115800-30119200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:30115800-30119400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:30115800-30119600	Weak transcription	Adipose Nuclei	Adipose
21	chr15:30115800-30119800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:30116000-30118800	Weak transcription	Brain Substantia Nigra	brain
23	chr15:30116000-30118800	Weak transcription	Fetal Heart	heart
24	chr15:30116000-30118800	Weak transcription	Placenta	Placenta
25	chr15:30116000-30121000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:30116200-30119000	Weak transcription	Right Ventricle	heart
27	chr15:30116400-30118000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:30116400-30118400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr15:30116400-30118600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr15:30116400-30119200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr15:30116600-30118000	Enhancers	NHEK	skin
32	chr15:30116600-30118200	Enhancers	HUVEC	blood vessel
33	chr15:30116600-30118400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr15:30116600-30118800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr15:30116600-30119200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:30116800-30117800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:30116800-30118000	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr15:30116800-30118400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr15:30116800-30119400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:30117200-30117800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr15:30117200-30118000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:30117200-30118000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:30117200-30118000	Enhancers	Osteobl	bone
44	chr15:30117400-30117800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:30117400-30117800	Enhancers	Brain Cingulate Gyrus	brain
46	chr15:30117400-30117800	Enhancers	NHLF	lung
47	chr15:30117400-30118000	Enhancers	A549	lung
48	chr15:30117400-30118000	Enhancers	Dnd41	blood
49	chr15:30117400-30118000	Enhancers	NH-A	brain
50	chr15:30117400-30118800	Enhancers	Fetal Lung	lung

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