Variant report

Variant	rs16972969
Chromosome Location	chr15:42563218-42563219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr15:42563146-42563297	SH-SY5Y	brain:	n/a	n/a
2	NR2F2	chr15:42562650-42563747	MCF-7	breast:	n/a	n/a
3	ESR1	chr15:42563154-42563744	T-47D	breast:	n/a	n/a
4	ESR1	chr15:42563176-42563704	T-47D	breast:	n/a	n/a
5	ESR1	chr15:42563172-42563707	T-47D	breast:	n/a	n/a
6	SIN3AK20	chr15:42562669-42563860	MCF-7	breast:	n/a	n/a
7	SIN3AK20	chr15:42563095-42563787	MCF-7	breast:	n/a	n/a
8	GATA3	chr15:42563181-42563751	T-47D	breast:	n/a	n/a
9	ESR1	chr15:42563177-42563692	T-47D	breast:	n/a	n/a
10	GATA3	chr15:42562631-42563762	T-47D	breast:	n/a	n/a
11	FOXA1	chr15:42563209-42563994	T-47D	breast:	n/a	chr15:42563526-42563541
12	TCF7L2	chr15:42562848-42563634	MCF-7	breast:	n/a	n/a
13	JUND	chr15:42562630-42563838	T-47D	breast:	n/a	n/a
14	MYC	chr15:42563076-42563233	MCF10A-Er-Src	breast:	n/a	n/a
15	GATA3	chr15:42562662-42563756	MCF-7	breast:	n/a	n/a
16	GATA3	chr15:42562688-42563813	MCF-7	breast:	n/a	n/a
17	JUND	chr15:42563141-42563634	T-47D	breast:	n/a	n/a
18	GATA3	chr15:42562875-42563662	MCF-7	breast:	n/a	n/a
19	EP300	chr15:42563119-42563813	T-47D	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:42559733..42563310-chr15:42678634..42681534,3	K562	blood:
2	chr15:42544904..42547005-chr15:42561537..42563318,2	K562	blood:
3	chr15:42563158..42565885-chr15:42567865..42572400,4	MCF-7	breast:

No data

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

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16972927	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16972930	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973015	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973018	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973022	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973177	0.83[EUR][1000 genomes]
rs16973182	0.83[EUR][1000 genomes]
rs16973184	0.83[EUR][1000 genomes]
rs16973188	0.83[EUR][1000 genomes]
rs16973200	1.00[EUR][1000 genomes]
rs16973206	0.83[EUR][1000 genomes]
rs17593	0.83[EUR][1000 genomes]
rs28364383	0.83[EUR][1000 genomes]
rs28364387	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364399	1.00[EUR][1000 genomes]
rs28364423	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4307925	0.83[EUR][1000 genomes]
rs4486855	0.83[EUR][1000 genomes]
rs4516202	0.83[EUR][1000 genomes]
rs7167683	0.83[EUR][1000 genomes]
rs7174880	0.83[EUR][1000 genomes]
rs728507	0.83[EUR][1000 genomes]
rs728508	0.83[EUR][1000 genomes]
rs728509	0.83[EUR][1000 genomes]
rs728510	1.00[EUR][1000 genomes]
rs8024452	0.83[EUR][1000 genomes]
rs8026890	0.83[EUR][1000 genomes]
rs8027800	0.83[EUR][1000 genomes]
rs8033108	1.00[EUR][1000 genomes]
rs8033734	0.83[EUR][1000 genomes]
rs8033882	0.83[EUR][1000 genomes]
rs8033960	0.83[EUR][1000 genomes]
rs8035332	0.83[EUR][1000 genomes]
rs8035521	0.83[EUR][1000 genomes]
rs8038771	0.83[EUR][1000 genomes]
rs8038967	0.83[EUR][1000 genomes]
rs8039470	0.83[EUR][1000 genomes]
rs8040129	0.83[EUR][1000 genomes]
rs8040726	1.00[EUR][1000 genomes]
rs934877	1.00[AMR][1000 genomes];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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42545600-42563400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:42546000-42564600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:42546200-42564600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:42547000-42564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:42547600-42563400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:42549600-42564400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:42551000-42563400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:42551800-42564600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:42552400-42563400	Weak transcription	Brain Angular Gyrus	brain
10	chr15:42552600-42564600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:42552600-42565000	Weak transcription	Gastric	stomach
12	chr15:42552600-42565200	Weak transcription	Spleen	Spleen
13	chr15:42552800-42564600	Weak transcription	Aorta	Aorta
14	chr15:42552800-42564600	Weak transcription	Esophagus	oesophagus
15	chr15:42552800-42564600	Weak transcription	Right Ventricle	heart
16	chr15:42556000-42563600	Weak transcription	Fetal Stomach	stomach
17	chr15:42556000-42564600	Weak transcription	Lung	lung
18	chr15:42556000-42565000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:42556200-42564600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr15:42557200-42563400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:42557800-42563400	Weak transcription	Fetal Brain Female	brain
22	chr15:42558400-42564200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:42558400-42564600	Weak transcription	Psoas Muscle	Psoas
24	chr15:42558600-42563400	Weak transcription	Brain Germinal Matrix	brain
25	chr15:42558600-42564600	Weak transcription	Thymus	Thymus
26	chr15:42559200-42563400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:42559400-42564400	Weak transcription	Fetal Muscle Leg	muscle
28	chr15:42559400-42564400	Weak transcription	HSMMtube	muscle
29	chr15:42559400-42564600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr15:42559800-42564200	Weak transcription	Fetal Kidney	kidney
31	chr15:42560400-42563400	Weak transcription	Primary T cells from cord blood	blood
32	chr15:42560400-42563400	Weak transcription	Fetal Lung	lung
33	chr15:42560400-42563400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:42560600-42564400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr15:42560600-42564600	Weak transcription	Placenta	Placenta
36	chr15:42560800-42563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:42560800-42564400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:42560800-42564600	Weak transcription	Fetal Thymus	thymus
39	chr15:42561200-42563400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:42561200-42563400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:42561200-42563400	Weak transcription	A549	lung
42	chr15:42561200-42564400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:42561400-42563400	Enhancers	Liver	Liver
44	chr15:42561400-42563400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr15:42561400-42564200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:42561800-42563400	Weak transcription	Primary B cells from cord blood	blood
47	chr15:42561800-42563400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:42562400-42563400	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr15:42562400-42564200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr15:42562400-42564400	Enhancers	Adipose Nuclei	Adipose

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