Variant report

Variant	rs6493031
Chromosome Location	chr15:42563838-42563839
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	POLR2A	chr15:42563764-42563976	MCF10A-Er-Src	breast:	n/a	n/a
2	SIN3AK20	chr15:42562669-42563860	MCF-7	breast:	n/a	n/a
3	FOXA1	chr15:42563209-42563994	T-47D	breast:	n/a	chr15:42563526-42563541
4	JUND	chr15:42562630-42563838	T-47D	breast:	n/a	n/a
5	FOXA1	chr15:42563258-42563921	T-47D	breast:	n/a	chr15:42563526-42563541

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42563158..42565885-chr15:42567865..42572400,4	MCF-7	breast:
2	chr15:42563255..42565132-chr15:42636659..42638368,2	K562	blood:

Variant related genes	Relation type
TMEM87A	TF binding region
GANC	TF binding region
ENSG00000214013	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11070367	1.00[EUR][1000 genomes]
rs11070371	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11633276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11856807	1.00[EUR][1000 genomes]
rs12102204	1.00[EUR][1000 genomes]
rs12902924	1.00[EUR][1000 genomes]
rs1659214	1.00[EUR][1000 genomes]
rs1659216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1659220	1.00[EUR][1000 genomes]
rs1659223	1.00[EUR][1000 genomes]
rs1659225	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2289293	1.00[EUR][1000 genomes]
rs2289297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2412675	1.00[EUR][1000 genomes]
rs2412676	1.00[EUR][1000 genomes]
rs2412678	1.00[EUR][1000 genomes]
rs2412683	1.00[EUR][1000 genomes]
rs2412684	1.00[EUR][1000 genomes]
rs2412689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2412694	1.00[EUR][1000 genomes]
rs2412695	1.00[EUR][1000 genomes]
rs2578651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2620372	1.00[EUR][1000 genomes]
rs28364379	1.00[EUR][1000 genomes]
rs28364398	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364400	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364462	1.00[EUR][1000 genomes]
rs28364472	1.00[EUR][1000 genomes]
rs28364491	1.00[EUR][1000 genomes]
rs28364495	1.00[EUR][1000 genomes]
rs28364498	1.00[EUR][1000 genomes]
rs28364500	1.00[EUR][1000 genomes]
rs28364503	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364504	1.00[EUR][1000 genomes]
rs28364507	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364509	1.00[EUR][1000 genomes]
rs28364511	1.00[EUR][1000 genomes]
rs28364519	1.00[EUR][1000 genomes]
rs28364522	1.00[EUR][1000 genomes]
rs28364523	1.00[EUR][1000 genomes]
rs28364524	1.00[EUR][1000 genomes]
rs28364526	1.00[EUR][1000 genomes]
rs28364540	1.00[EUR][1000 genomes]
rs28364541	1.00[EUR][1000 genomes]
rs28364544	1.00[EUR][1000 genomes]
rs28364557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28489155	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28621687	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28745879	1.00[EUR][1000 genomes]
rs2899044	1.00[EUR][1000 genomes]
rs3743002	1.00[EUR][1000 genomes]
rs3803342	1.00[EUR][1000 genomes]
rs4556762	1.00[EUR][1000 genomes]
rs4923936	1.00[EUR][1000 genomes]
rs4923937	1.00[EUR][1000 genomes]
rs4923939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924640	1.00[EUR][1000 genomes]
rs4924641	1.00[EUR][1000 genomes]
rs4924642	1.00[EUR][1000 genomes]
rs4924643	1.00[EUR][1000 genomes]
rs4924649	1.00[EUR][1000 genomes]
rs4924657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924670	1.00[EUR][1000 genomes]
rs5028173	1.00[EUR][1000 genomes]
rs595661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493024	1.00[EUR][1000 genomes]
rs6493026	1.00[EUR][1000 genomes]
rs6493034	1.00[EUR][1000 genomes]
rs6493038	1.00[EUR][1000 genomes]
rs6493041	1.00[EUR][1000 genomes]
rs655704	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67384392	1.00[EUR][1000 genomes]
rs685447	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7161982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164484	1.00[EUR][1000 genomes]
rs7169553	1.00[EUR][1000 genomes]
rs7170943	1.00[EUR][1000 genomes]
rs7177193	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7177463	1.00[EUR][1000 genomes]
rs7178396	1.00[EUR][1000 genomes]
rs7181758	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7182777	1.00[EUR][1000 genomes]
rs7183399	1.00[EUR][1000 genomes]
rs7183843	1.00[EUR][1000 genomes]
rs8023568	1.00[EUR][1000 genomes]
rs8023678	1.00[EUR][1000 genomes]
rs8040720	1.00[EUR][1000 genomes]
rs8042603	1.00[EUR][1000 genomes]
rs8043033	1.00[EUR][1000 genomes]
rs936603	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920851	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42546000-42564600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:42546200-42564600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:42547000-42564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:42549600-42564400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:42551800-42564600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:42552600-42564600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:42552600-42565000	Weak transcription	Gastric	stomach
8	chr15:42552600-42565200	Weak transcription	Spleen	Spleen
9	chr15:42552800-42564600	Weak transcription	Aorta	Aorta
10	chr15:42552800-42564600	Weak transcription	Esophagus	oesophagus
11	chr15:42552800-42564600	Weak transcription	Right Ventricle	heart
12	chr15:42556000-42564600	Weak transcription	Lung	lung
13	chr15:42556000-42565000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:42556200-42564600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:42558400-42564200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:42558400-42564600	Weak transcription	Psoas Muscle	Psoas
17	chr15:42558600-42564600	Weak transcription	Thymus	Thymus
18	chr15:42559400-42564400	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:42559400-42564400	Weak transcription	HSMMtube	muscle
20	chr15:42559400-42564600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:42559800-42564200	Weak transcription	Fetal Kidney	kidney
22	chr15:42560600-42564400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:42560600-42564600	Weak transcription	Placenta	Placenta
24	chr15:42560800-42564400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:42560800-42564600	Weak transcription	Fetal Thymus	thymus
26	chr15:42561200-42564400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:42561400-42564200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:42562400-42564200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr15:42562400-42564400	Enhancers	Adipose Nuclei	Adipose
30	chr15:42562400-42564600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr15:42562600-42564400	Enhancers	Brain Anterior Caudate	brain
32	chr15:42562600-42564600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr15:42562600-42564600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr15:42562600-42564600	Weak transcription	Colonic Mucosa	Colon
35	chr15:42562600-42564600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:42562800-42564000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:42562800-42564400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:42562800-42564400	Enhancers	Brain Hippocampus Middle	brain
39	chr15:42562800-42564400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr15:42562800-42564600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr15:42562800-42564600	Weak transcription	Left Ventricle	heart
42	chr15:42562800-42564600	Weak transcription	Ovary	ovary
43	chr15:42562800-42564800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:42562800-42565000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:42562800-42565000	Weak transcription	Pancreas	Pancrea
46	chr15:42562800-42566600	Active TSS	NHLF	lung
47	chr15:42563000-42564000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:42563000-42564000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:42563000-42564000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:42563000-42564000	Genic enhancers	HSMM	muscle

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