Variant report

Variant	rs11973038
Chromosome Location	chr7:47991245-47991246
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	ZNF217	chr7:47990983-47991600	MCF-7	breast:	n/a	n/a
2	NR2F2	chr7:47990907-47991815	MCF-7	breast:	n/a	n/a
3	GATA3	chr7:47990171-47991966	MCF-7	breast:	n/a	chr7:47991804-47991820 chr7:47991802-47991823 chr7:47991701-47991710 chr7:47991804-47991820
4	FOXA1	chr7:47990988-47991342	HepG2	liver:	n/a	chr7:47991171-47991186
5	FOXA1	chr7:47990907-47991464	HepG2	liver:	n/a	chr7:47991171-47991186
6	FOXA1	chr7:47990850-47991382	HepG2	liver:	n/a	chr7:47991171-47991186
7	GATA3	chr7:47991007-47992230	T-47D	breast:	n/a	chr7:47991804-47991820 chr7:47991802-47991823 chr7:47991701-47991710 chr7:47991804-47991820
8	FOXA2	chr7:47991020-47991480	A549	lung:	n/a	n/a
9	HDAC2	chr7:47990942-47991735	MCF-7	breast:	n/a	chr7:47991544-47991552 chr7:47991546-47991560
10	FOXA2	chr7:47990660-47991584	HepG2	liver:	n/a	n/a
11	GATA3	chr7:47991116-47991568	MCF-7	breast:	n/a	n/a
12	RXRA	chr7:47990985-47991280	HepG2	liver:	n/a	n/a
13	GATA3	chr7:47990892-47992063	MCF-7	breast:	n/a	chr7:47991804-47991820 chr7:47991802-47991823 chr7:47991701-47991710 chr7:47991804-47991820
14	GATA3	chr7:47990944-47992202	T-47D	breast:	n/a	chr7:47991804-47991820 chr7:47991802-47991823 chr7:47991701-47991710 chr7:47991804-47991820
15	TEAD4	chr7:47990870-47991365	HepG2	liver:	n/a	n/a
16	GATA3	chr7:47990881-47992086	MCF-7	breast:	n/a	chr7:47991804-47991820 chr7:47991802-47991823 chr7:47991701-47991710 chr7:47991804-47991820
17	FOXA2	chr7:47990939-47991328	HepG2	liver:	n/a	n/a
18	FOXA1	chr7:47990870-47991572	T-47D	breast:	n/a	chr7:47991171-47991186
19	FOXA1	chr7:47990989-47991621	T-47D	breast:	n/a	chr7:47991171-47991186
20	HDAC2	chr7:47991001-47991284	HepG2	liver:	n/a	n/a
21	EP300	chr7:47990891-47991634	T-47D	breast:	n/a	n/a
22	ZEB1	chr7:47990850-47991447	HepG2	liver:	n/a	n/a
23	ZEB1	chr7:47990803-47991476	HepG2	liver:	n/a	n/a
24	FOXA1	chr7:47990877-47991410	HepG2	liver:	n/a	chr7:47991171-47991186
25	SIN3AK20	chr7:47990845-47991823	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
PKD1L1	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2254324	0.82[ASN][1000 genomes]
rs2307254	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3176498	0.88[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3176499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3176593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3176602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer 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
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47967600-47993400	Weak transcription	Brain Anterior Caudate	brain
3	chr7:47977400-48000600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:47978400-47993800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:47978400-47994000	Weak transcription	Fetal Thymus	thymus
6	chr7:47978600-47992600	Weak transcription	Primary B cells from cord blood	blood
7	chr7:47980600-47994200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:47980800-47993000	Weak transcription	Fetal Stomach	stomach
9	chr7:47981200-47991400	Weak transcription	Colonic Mucosa	Colon
10	chr7:47981200-47995600	Weak transcription	Aorta	Aorta
11	chr7:47981800-47991600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:47982000-47994000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:47982000-47994000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr7:47982000-47994200	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr7:47982000-47999400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:47982400-47992600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr7:47983600-47993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:47983600-47993800	Weak transcription	Osteobl	bone
19	chr7:47983600-47994400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:47983600-48001000	Weak transcription	NHLF	lung
21	chr7:47983800-47993600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:47983800-47993800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:47983800-47995800	Weak transcription	NHDF-Ad	bronchial
24	chr7:47984800-47993800	Weak transcription	Esophagus	oesophagus
25	chr7:47984800-47996000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:47985000-48001400	Weak transcription	Hela-S3	cervix
27	chr7:47985200-47995000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:47985200-47995400	Weak transcription	Fetal Heart	heart
29	chr7:47985400-47993800	Weak transcription	Placenta	Placenta
30	chr7:47985400-47995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:47985600-48000600	Weak transcription	Ovary	ovary
32	chr7:47986200-47991400	Weak transcription	Pancreas	Pancrea
33	chr7:47986400-47993000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:47986400-47993400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:47986400-47993800	Weak transcription	HMEC	breast
36	chr7:47986400-47994200	Weak transcription	Small Intestine	intestine
37	chr7:47986400-48003800	Weak transcription	Fetal Brain Male	brain
38	chr7:47986600-47993600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr7:47986600-47994000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:47986800-48001800	Weak transcription	NHEK	skin
41	chr7:47987200-47993200	Weak transcription	Fetal Intestine Small	intestine
42	chr7:47987200-47993800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr7:47987200-47994400	Weak transcription	Right Ventricle	heart
44	chr7:47987800-47994000	Weak transcription	Lung	lung
45	chr7:47988200-47993400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:47988600-47993000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr7:47988600-47993600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:47988600-47994600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:47988800-47994200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr7:47989400-47991800	Enhancers	HUES48 Cell Line	embryonic stem cell

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