Variant report

Variant	rs35245331
Chromosome Location	chr4:87924755-87924756
allele	G/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	STAT3	chr4:87924561-87924759	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87918478..87926067-chr4:87926181..87931063,13	MCF-7	breast:
2	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:

Variant related genes	Relation type
AFF1	TF binding region
ENSG00000235043	Chromatin interaction
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10489044	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10516787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13109968	1.00[AFR][1000 genomes]
rs13110344	1.00[AFR][1000 genomes]
rs13136338	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13136465	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13140610	0.83[AFR][1000 genomes]
rs17702203	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33983129	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34140562	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34227282	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34709431	1.00[AFR][1000 genomes]
rs34745873	1.00[AFR][1000 genomes]
rs35182728	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35653846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35812445	1.00[AFR][1000 genomes]
rs35849753	0.83[AFR][1000 genomes]
rs35886751	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41525049	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs431836	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62305658	1.00[AFR][1000 genomes]
rs62306466	1.00[AFR][1000 genomes]
rs62306480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62306505	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62306508	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62306509	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62306510	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62306511	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62306514	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6853425	0.83[AFR][1000 genomes]
rs767314	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[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	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87899200-87925800	Weak transcription	Hela-S3	cervix
3	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:87903200-87926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:87904200-87926200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:87914200-87927400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:87916000-87926200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:87916200-87927200	Weak transcription	Esophagus	oesophagus
9	chr4:87916400-87926200	Weak transcription	Fetal Intestine Large	intestine
10	chr4:87916400-87927200	Weak transcription	Gastric	stomach
11	chr4:87918000-87925400	Enhancers	Placenta	Placenta
12	chr4:87919000-87927000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr4:87919200-87927400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:87919400-87925400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr4:87920600-87926000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:87920800-87926000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr4:87920800-87926000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr4:87920800-87926200	Weak transcription	Thymus	Thymus
19	chr4:87921000-87926400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:87921200-87925800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:87921200-87925800	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:87921200-87926200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:87921200-87926200	Weak transcription	Left Ventricle	heart
24	chr4:87921200-87926200	Weak transcription	Spleen	Spleen
25	chr4:87921200-87926400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:87921200-87927000	Weak transcription	Right Ventricle	heart
27	chr4:87921400-87925800	Weak transcription	Primary T cells from cord blood	blood
28	chr4:87921400-87926000	Weak transcription	A549	lung
29	chr4:87921400-87926200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:87921400-87926400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:87921600-87924800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:87921600-87925000	Weak transcription	GM12878-XiMat	blood
33	chr4:87921600-87925800	Weak transcription	Primary B cells from cord blood	blood
34	chr4:87921600-87925800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:87921600-87926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:87921600-87926200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:87921600-87926200	Weak transcription	Fetal Thymus	thymus
38	chr4:87921600-87926200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:87921600-87926400	Weak transcription	Brain Substantia Nigra	brain
40	chr4:87921600-87926400	Weak transcription	Stomach Mucosa	stomach
41	chr4:87921600-87926400	Weak transcription	K562	blood
42	chr4:87921800-87925200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr4:87921800-87925800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:87921800-87926000	Weak transcription	NHLF	lung
45	chr4:87921800-87926200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr4:87921800-87926200	Weak transcription	HUVEC	blood vessel
47	chr4:87921800-87926600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:87921800-87926600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:87922000-87924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr4:87922000-87926200	Weak transcription	Duodenum Mucosa	Duodenum

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