Variant report

Variant	rs2241648
Chromosome Location	chr15:34158529-34158530
allele	C/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	GATA3	chr15:34158212-34158889	T-47D	breast:	n/a	chr15:34158413-34158423
2	ZNF217	chr15:34158205-34159028	MCF-7	breast:	n/a	n/a
3	GATA3	chr15:34158142-34159069	MCF-7	breast:	n/a	chr15:34158413-34158423
4	TCF7L2	chr15:34158293-34158750	PANC-1	pancreas:	n/a	n/a
5	GATA3	chr15:34158297-34158940	MCF-7	breast:	n/a	chr15:34158413-34158423
6	FOXA1	chr15:34158200-34158909	T-47D	breast:	n/a	n/a
7	SRF	chr15:34158295-34159140	MCF-7	breast:	n/a	n/a
8	GATA3	chr15:34158262-34158975	MCF-7	breast:	n/a	chr15:34158413-34158423
9	HDAC2	chr15:34158304-34158893	MCF-7	breast:	n/a	chr15:34158410-34158424
10	SIN3AK20	chr15:34158161-34159015	MCF-7	breast:	n/a	n/a
11	TCF7L2	chr15:34158299-34158911	MCF-7	breast:	n/a	n/a
12	SRF	chr15:34158527-34159046	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr15:34158468-34158863	H1-neurons	neurons:	n/a	n/a
14	EP300	chr15:34158139-34158855	T-47D	breast:	n/a	n/a
15	JUND	chr15:34158178-34158884	T-47D	breast:	n/a	chr15:34158359-34158370
16	JUND	chr15:34158115-34158985	T-47D	breast:	n/a	chr15:34158359-34158370
17	EP300	chr15:34158250-34158650	T-47D	breast:	n/a	n/a
18	SIN3AK20	chr15:34158130-34159034	MCF-7	breast:	n/a	n/a
19	GATA3	chr15:34158322-34158874	MCF-7	breast:	n/a	chr15:34158413-34158423
20	GATA3	chr15:34158168-34158859	T-47D	breast:	n/a	chr15:34158413-34158423
21	SRF	chr15:34158489-34159037	MCF-7	breast:	n/a	n/a
22	FOXA1	chr15:34158196-34158939	T-47D	breast:	n/a	n/a

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	AVEN	hsa-miR-30a-5p	chr15:34158513-34158534

Variant related genes	Relation type
ENSG00000259287	TF binding region
AVEN	miRNA target site

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10459652	0.88[ASN][1000 genomes]
rs12439280	0.95[CHB][hapmap];0.85[CHD][hapmap]
rs2278072	0.80[CHB][hapmap]
rs2278314	0.80[CHB][hapmap];0.92[GIH][hapmap]
rs2303309	0.84[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2303868	1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap]
rs2303870	0.93[CHB][hapmap]
rs3794590	1.00[CEU][hapmap]
rs489349	1.00[CEU][hapmap]
rs891343	0.80[CHB][hapmap]
rs891344	0.85[CHB][hapmap]

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	nsv1043046	chr15:33714908-34321330	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases
4	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv568921	chr15:34046635-34247622	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1044844	chr15:34065524-34296829	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34130800-34158600	Weak transcription	Brain Germinal Matrix	brain
2	chr15:34137400-34164200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:34139800-34164200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:34142400-34168600	Weak transcription	Esophagus	oesophagus
5	chr15:34143000-34165000	Weak transcription	Psoas Muscle	Psoas
6	chr15:34143400-34160400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:34143600-34164200	Weak transcription	Brain Angular Gyrus	brain
8	chr15:34145000-34161200	Weak transcription	Small Intestine	intestine
9	chr15:34145600-34158600	Weak transcription	HSMM	muscle
10	chr15:34146800-34164000	Weak transcription	Right Ventricle	heart
11	chr15:34147200-34162400	Weak transcription	Pancreas	Pancrea
12	chr15:34147400-34164200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:34148600-34159400	Weak transcription	Lung	lung
14	chr15:34149400-34165800	Weak transcription	Fetal Intestine Small	intestine
15	chr15:34150200-34164000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:34150200-34164000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr15:34150800-34167400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:34151600-34161000	Weak transcription	Thymus	Thymus
19	chr15:34152000-34164200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:34152400-34161800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:34152400-34162400	Weak transcription	Spleen	Spleen
22	chr15:34152400-34167600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:34152600-34160000	Weak transcription	Fetal Brain Female	brain
24	chr15:34152600-34164200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:34152600-34164200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:34153200-34164200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr15:34153400-34166400	Weak transcription	HMEC	breast
28	chr15:34153600-34158600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:34153600-34161000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:34153600-34164400	Weak transcription	NHDF-Ad	bronchial
31	chr15:34153600-34165000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:34153600-34166000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:34153600-34166000	Weak transcription	NHEK	skin
34	chr15:34153800-34159200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr15:34153800-34164200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:34153800-34164400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:34153800-34164600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:34154200-34160200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr15:34155200-34159800	Weak transcription	HUVEC	blood vessel
40	chr15:34155600-34160000	Strong transcription	Fetal Muscle Leg	muscle
41	chr15:34155600-34169600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:34156000-34159000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr15:34156000-34163800	Weak transcription	Fetal Brain Male	brain
44	chr15:34156200-34158600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:34156200-34159800	Strong transcription	Adipose Nuclei	Adipose
46	chr15:34156200-34160400	Strong transcription	Primary T cells from cord blood	blood
47	chr15:34156400-34158600	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr15:34156400-34158800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:34156400-34158800	Weak transcription	HepG2	liver
50	chr15:34156400-34159600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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