Variant report

Variant	rs375779
Chromosome Location	chr5:9523996-9523997
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	SIN3AK20	chr5:9523391-9524251	MCF-7	breast:	n/a	n/a
2	GATA3	chr5:9523226-9524084	MCF-7	breast:	n/a	n/a
3	JUND	chr5:9523399-9524059	MCF-7	breast:	n/a	chr5:9523702-9523712 chr5:9523684-9523692 chr5:9523701-9523713 chr5:9523702-9523712 chr5:9523683-9523694 chr5:9523704-9523711 chr5:9523684-9523691 chr5:9523701-9523712 chr5:9523685-9523696 chr5:9523703-9523712 chr5:9523702-9523711 chr5:9523682-9523693 chr5:9523684-9523692
4	JUND	chr5:9523407-9524036	MCF-7	breast:	n/a	chr5:9523702-9523712 chr5:9523684-9523692 chr5:9523701-9523713 chr5:9523702-9523712 chr5:9523683-9523694 chr5:9523704-9523711 chr5:9523684-9523691 chr5:9523701-9523712 chr5:9523685-9523696 chr5:9523703-9523712 chr5:9523702-9523711 chr5:9523682-9523693 chr5:9523684-9523692
5	GATA3	chr5:9523120-9524120	MCF-7	breast:	n/a	n/a
6	FOSL2	chr5:9523391-9524015	MCF-7	breast:	n/a	chr5:9523702-9523712 chr5:9523684-9523692 chr5:9523701-9523713 chr5:9523702-9523712 chr5:9523683-9523694 chr5:9523704-9523711 chr5:9523684-9523691 chr5:9523685-9523696 chr5:9523703-9523712 chr5:9523702-9523711 chr5:9523684-9523692
7	NR2F2	chr5:9523408-9524236	MCF-7	breast:	n/a	n/a
8	SIN3AK20	chr5:9523521-9524110	MCF-7	breast:	n/a	n/a
9	NR2F2	chr5:9523413-9524056	MCF-7	breast:	n/a	n/a
10	JUND	chr5:9523529-9524038	SK-N-SH	brain:	n/a	chr5:9523702-9523712 chr5:9523684-9523692 chr5:9523701-9523713 chr5:9523702-9523712 chr5:9523683-9523694 chr5:9523704-9523711 chr5:9523684-9523691 chr5:9523701-9523712 chr5:9523685-9523696 chr5:9523703-9523712 chr5:9523702-9523711 chr5:9523682-9523693 chr5:9523684-9523692
11	HDAC2	chr5:9523572-9524172	MCF-7	breast:	n/a	chr5:9523841-9523849

No.	Distal block	Cell Line	Cell type
1	chr5:9519723..9521452-chr5:9523293..9526016,2	MCF-7	breast:
2	chr5:9518291..9521025-chr5:9523342..9525651,2	K562	blood:
3	chr5:9522895..9524468-chr5:9544584..9546294,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250001	TF binding region
ENSG00000112902	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs13178837	0.96[EUR][1000 genomes]
rs174863	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2458362	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268544	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268545	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268546	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268547	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs268548	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268549	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268551	0.96[EUR][1000 genomes]
rs268552	0.95[EUR][1000 genomes]
rs371458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756733	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs377791	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382409	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398533	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406583	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420819	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435329	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439869	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446573	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453742	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455353	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455538	0.96[EUR][1000 genomes]
rs455757	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456058	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456400	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457203	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459659	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459789	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs459793	0.96[EUR][1000 genomes]
rs460887	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs461321	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs461415	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs461700	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs461907	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462057	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462473	0.96[EUR][1000 genomes]
rs462652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs463004	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs463029	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464267	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464616	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464975	0.82[ASN][1000 genomes]
rs465205	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs465991	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466158	0.96[EUR][1000 genomes]
rs466667	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs466883	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630768	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS 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	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9499200-9528600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:9513000-9532800	Weak transcription	Fetal Stomach	stomach
3	chr5:9513000-9535200	Weak transcription	Aorta	Aorta
4	chr5:9518600-9524400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:9518800-9525200	Weak transcription	Small Intestine	intestine
6	chr5:9520400-9532800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:9520600-9526800	Weak transcription	Left Ventricle	heart
8	chr5:9520800-9524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:9521200-9527000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:9521200-9544400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:9522200-9524200	Weak transcription	Right Ventricle	heart
12	chr5:9522200-9528600	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:9522200-9529200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:9522400-9525400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:9522400-9526600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:9522600-9529400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:9522800-9527800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:9523200-9524000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:9523200-9524000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:9523200-9524000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:9523200-9524000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:9523200-9524000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:9523200-9524000	Enhancers	NH-A	brain
24	chr5:9523200-9524000	Enhancers	NHLF	lung
25	chr5:9523200-9524200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr5:9523200-9524400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:9523400-9524000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:9523400-9524000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:9523400-9524000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:9523400-9524000	Enhancers	Fetal Kidney	kidney
31	chr5:9523400-9524200	Enhancers	Osteobl	bone
32	chr5:9523400-9524600	Enhancers	NHDF-Ad	bronchial
33	chr5:9523400-9525200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:9523600-9524000	Enhancers	Pancreas	Pancrea
35	chr5:9523600-9524000	Enhancers	HMEC	breast
36	chr5:9523600-9524600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:9523600-9525800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr5:9523600-9525800	Enhancers	Fetal Heart	heart
39	chr5:9523600-9528400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr5:9523800-9524000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:9523800-9524000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr5:9523800-9524600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:9523800-9525800	Enhancers	Pancreatic Islets	Pancreatic Islet

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