Variant report

Variant	rs7172939
Chromosome Location	chr15:52436590-52436591
allele	A/G
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	TEAD4	chr15:52435977-52436750	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr15:52436024-52436602	SK-N-SH	brain:	n/a	n/a
3	TEAD4	chr15:52435901-52436799	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr15:52435851-52437334	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr15:52435845-52436631	U87	brain:	n/a	n/a
6	RCOR1	chr15:52435771-52437402	IMR90	lung:	n/a	n/a
7	FOXM1	chr15:52435834-52436590	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr15:52435738-52437411	SK-N-SH	brain:	n/a	n/a
9	RCOR1	chr15:52436084-52436702	Hela-S3	cervix:	n/a	n/a
10	JUND	chr15:52435960-52436724	SK-N-SH	brain:	n/a	chr15:52436307-52436318
11	POLR2A	chr15:52435845-52436681	U87	brain:	n/a	n/a
12	JUN	chr15:52435790-52436599	Hela-S3	cervix:	n/a	n/a
13	GATA3	chr15:52435895-52436725	SK-N-SH	brain:	n/a	chr15:52435922-52435943 chr15:52435927-52435936
14	NFIC	chr15:52435908-52436710	SK-N-SH	brain:	n/a	n/a
15	FOSL2	chr15:52435930-52437356	SK-N-SH	brain:	n/a	n/a
16	EP300	chr15:52435944-52436712	Hela-S3	cervix:	n/a	n/a
17	CEBPB	chr15:52435814-52437236	Hela-S3	cervix:	n/a	n/a
18	EP300	chr15:52435793-52436703	SK-N-SH	brain:	n/a	n/a
19	MAZ	chr15:52436002-52436786	IMR90	lung:	n/a	n/a
20	PBX3	chr15:52435930-52436626	SK-N-SH	brain:	n/a	chr15:52436176-52436196
21	GATA3	chr15:52435830-52437376	SK-N-SH	brain:	n/a	chr15:52435922-52435943 chr15:52435927-52435936
22	RXRA	chr15:52436011-52436691	SK-N-SH	brain:	n/a	n/a
23	JUND	chr15:52435838-52436609	Hela-S3	cervix:	n/a	chr15:52436307-52436318
24	STAT3	chr15:52435881-52436627	Hela-S3	cervix:	n/a	chr15:52436026-52436037 chr15:52436202-52436210
25	PBX3	chr15:52435871-52436657	SK-N-SH	brain:	n/a	chr15:52436176-52436196
26	JUND	chr15:52435749-52437338	SK-N-SH	brain:	n/a	chr15:52436307-52436318
27	JUND	chr15:52435914-52436728	SK-N-SH	brain:	n/a	chr15:52436307-52436318
28	MAX	chr15:52435899-52436648	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr15:52435436-52436773	U87	brain:	n/a	n/a
30	POLR2A	chr15:52435340-52436752	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52433182..52434903-chr15:52435277..52437876,2	MCF-7	breast:

Variant related genes	Relation type
GNB5	TF binding region
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10400852	1.00[EUR][1000 genomes]
rs12443497	1.00[TSI][hapmap]
rs16953085	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964735	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16964737	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964750	1.00[EUR][1000 genomes]
rs16964770	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs2231296	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28656256	1.00[EUR][1000 genomes]
rs28663157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41494446	1.00[EUR][1000 genomes]
rs59195841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59289747	1.00[EUR][1000 genomes]
rs60397096	1.00[EUR][1000 genomes]
rs7163133	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164357	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7165157	1.00[EUR][1000 genomes]
rs7165527	1.00[EUR][1000 genomes]
rs7165708	1.00[EUR][1000 genomes]
rs7167133	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171700	1.00[EUR][1000 genomes]
rs7178038	1.00[EUR][1000 genomes]
rs730945	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402803	1.00[EUR][1000 genomes]
rs73402824	1.00[EUR][1000 genomes]
rs73402826	1.00[EUR][1000 genomes]
rs73402833	1.00[EUR][1000 genomes]
rs73402839	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402857	0.93[AFR][1000 genomes]
rs73402859	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402869	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73404813	1.00[EUR][1000 genomes]
rs8023921	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8024311	1.00[EUR][1000 genomes]
rs8024767	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8035146	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8040458	1.00[EUR][1000 genomes]
rs8041042	1.00[EUR][1000 genomes]
rs8041128	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8041233	1.00[EUR][1000 genomes]
rs8041355	1.00[EUR][1000 genomes]
rs8041504	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
2	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
3	chr15:52410200-52441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:52410600-52441400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:52412000-52441200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:52423000-52436800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:52423000-52458200	Weak transcription	Dnd41	blood
9	chr15:52424000-52441200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:52427400-52441600	Weak transcription	Esophagus	oesophagus
11	chr15:52428800-52440600	Weak transcription	Spleen	Spleen
12	chr15:52429000-52446400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:52429000-52447200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:52429200-52447400	Strong transcription	Primary T cells from cord blood	blood
15	chr15:52429600-52438400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:52429600-52440600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:52429800-52436600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
19	chr15:52430000-52440800	Weak transcription	Brain Anterior Caudate	brain
20	chr15:52430000-52441400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:52430000-52442800	Weak transcription	Fetal Heart	heart
22	chr15:52430000-52445800	Weak transcription	Small Intestine	intestine
23	chr15:52430200-52437000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:52430200-52438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:52430200-52440600	Weak transcription	Fetal Intestine Small	intestine
26	chr15:52430200-52441000	Weak transcription	Gastric	stomach
27	chr15:52430200-52441800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:52430200-52442800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr15:52430200-52442800	Weak transcription	Right Ventricle	heart
30	chr15:52430200-52444800	Weak transcription	Left Ventricle	heart
31	chr15:52430200-52446600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:52430200-52457800	Weak transcription	Fetal Intestine Large	intestine
33	chr15:52430400-52441200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:52431000-52446200	Strong transcription	Primary B cells from cord blood	blood
35	chr15:52431200-52437200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:52431400-52446600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:52432200-52436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:52432200-52438600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:52432200-52443000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr15:52432200-52445400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:52432200-52453800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr15:52432200-52455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:52432200-52455200	Weak transcription	Colonic Mucosa	Colon
44	chr15:52432400-52439400	Weak transcription	Colon Smooth Muscle	Colon
45	chr15:52432400-52440400	Weak transcription	Adipose Nuclei	Adipose
46	chr15:52432600-52436800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr15:52432600-52441000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:52432600-52441600	Weak transcription	Brain Angular Gyrus	brain
49	chr15:52432800-52437000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr15:52433000-52436600	Weak transcription	A549	lung

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