Variant report

Variant	rs6495890
Chromosome Location	chr15:30026962-30026963
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	SP1	chr15:30026900-30028343	A549	lung:	n/a	n/a
2	TCF12	chr15:30026831-30029802	A549	lung:	n/a	n/a
3	GATA3	chr15:30026925-30028094	A549	lung:	n/a	chr15:30027991-30027998
4	EP300	chr15:30026905-30028297	A549	lung:	n/a	chr15:30027413-30027427 chr15:30028079-30028093 chr15:30027414-30027428 chr15:30027961-30027971 chr15:30027416-30027430
5	BATF	chr15:30026858-30027024	GM12878	blood:	n/a	chr15:30026966-30026977
6	EP300	chr15:30026890-30028172	A549	lung:	n/a	chr15:30027413-30027427 chr15:30028079-30028093 chr15:30027414-30027428 chr15:30027961-30027971 chr15:30027416-30027430
7	FOSL2	chr15:30026859-30029485	A549	lung:	n/a	chr15:30028999-30029010 chr15:30029054-30029063 chr15:30029055-30029063 chr15:30029052-30029063 chr15:30029055-30029062 chr15:30029054-30029064 chr15:30027410-30027422 chr15:30028075-30028087 chr15:30029055-30029064
8	SP1	chr15:30026854-30028220	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:30026202..30029026-chr15:30112927..30115291,2	MCF-7	breast:

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

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10152681	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10775231	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11073205	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11636849	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12438925	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12440211	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12440708	0.84[EUR][1000 genomes]
rs12441554	0.82[EUR][1000 genomes]
rs1383315	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1480503	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1585900	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1871678	0.84[EUR][1000 genomes]
rs2032	0.86[EUR][1000 genomes]
rs2229518	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2337167	0.82[EUR][1000 genomes]
rs2337170	0.85[ASN][1000 genomes]
rs2337171	0.80[ASN][1000 genomes]
rs260541	0.85[ASN][1000 genomes]
rs260543	0.80[ASN][1000 genomes]
rs28675809	0.84[EUR][1000 genomes]
rs2878893	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2878905	0.87[EUR][1000 genomes]
rs4073316	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4362339	0.84[EUR][1000 genomes]
rs4780258	0.80[EUR][1000 genomes]
rs4780259	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4780260	0.87[EUR][1000 genomes]
rs4780263	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6495914	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6495927	0.87[EUR][1000 genomes]
rs6495935	0.87[EUR][1000 genomes]
rs6495945	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7166786	0.86[EUR][1000 genomes]
rs7168919	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7170406	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7171815	0.86[EUR][1000 genomes]
rs7175819	0.84[EUR][1000 genomes]
rs7176476	0.87[EUR][1000 genomes]
rs7180387	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs767514	0.89[AMR][1000 genomes];0.96[EUR][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	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	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29989600-30027200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:29990200-30028400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:30014800-30028400	Strong transcription	NHEK	skin
4	chr15:30015000-30028400	Weak transcription	Stomach Mucosa	stomach
5	chr15:30015000-30035000	Strong transcription	Adipose Nuclei	Adipose
6	chr15:30015400-30028600	Strong transcription	HUVEC	blood vessel
7	chr15:30015600-30034800	Strong transcription	Fetal Muscle Leg	muscle
8	chr15:30015600-30035200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:30015600-30037600	Weak transcription	Small Intestine	intestine
10	chr15:30015800-30027200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:30015800-30027600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:30015800-30034400	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:30016600-30029800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr15:30016600-30035200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:30016600-30052000	Weak transcription	Spleen	Spleen
16	chr15:30016600-30068200	Weak transcription	Brain Germinal Matrix	brain
17	chr15:30016800-30027200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:30016800-30035600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:30017400-30035600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:30017600-30035400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:30017600-30041600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:30017600-30048600	Weak transcription	Fetal Brain Male	brain
23	chr15:30018200-30029400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:30018200-30030800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:30018200-30052000	Weak transcription	Gastric	stomach
26	chr15:30018400-30035800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:30018800-30028400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr15:30019000-30031200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr15:30019200-30035200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:30020200-30037000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr15:30021200-30061600	Weak transcription	Colonic Mucosa	Colon
32	chr15:30021400-30032400	Weak transcription	Pancreas	Pancrea
33	chr15:30021400-30097200	Weak transcription	Aorta	Aorta
34	chr15:30021600-30028600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:30022000-30029600	Strong transcription	Brain Anterior Caudate	brain
36	chr15:30022600-30028000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:30022600-30028600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:30022600-30029600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr15:30023000-30027400	Weak transcription	Fetal Intestine Small	intestine
40	chr15:30023000-30027400	Weak transcription	Fetal Stomach	stomach
41	chr15:30023000-30027400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:30023000-30027600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:30023000-30028400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:30023000-30032400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:30023000-30032400	Weak transcription	Lung	lung
46	chr15:30023800-30029600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:30024000-30027200	Strong transcription	Osteobl	bone
48	chr15:30024000-30031000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr15:30024000-30034400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:30024000-30035000	Strong transcription	Placenta	Placenta

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