Variant report

Variant	rs10935463
Chromosome Location	chr3:142167976-142167977
allele	A/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	POLR2A	chr3:142165803-142168021	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142164997..142168564-chr3:142170242..142173896,7	MCF-7	breast:
2	chr3:142166755..142169411-chr3:142174583..142176894,2	K562	blood:
3	chr3:142166774..142168881-chr3:142175818..142179023,4	MCF-7	breast:
4	chr3:142167068..142168704-chr3:142178358..142179911,2	K562	blood:

Variant related genes	Relation type
ENSG00000242479	TF binding region
XRN1	TF binding region
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1129391	0.81[EUR][1000 genomes]
rs11708470	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715514	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11916455	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12629713	0.81[EUR][1000 genomes]
rs12634255	0.80[EUR][1000 genomes]
rs12638158	0.80[EUR][1000 genomes]
rs12639363	0.81[EUR][1000 genomes]
rs13063075	0.84[EUR][1000 genomes]
rs13065800	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13066441	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13068397	0.80[EUR][1000 genomes]
rs13070239	0.81[EUR][1000 genomes]
rs13072355	0.80[EUR][1000 genomes]
rs13075259	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13085247	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13085261	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13089219	0.80[EUR][1000 genomes]
rs13092593	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13099184	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227929	0.81[EUR][1000 genomes]
rs2227931	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3923464	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4256152	0.89[EUR][1000 genomes]
rs4558780	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4582075	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440085	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6776402	0.81[EUR][1000 genomes]
rs7630115	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9829125	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer 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 target site	61 gene(s)	inside rSNPs	diseases
2	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1000083	chr3:141956718-142172666	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv528954	chr3:142164017-142219542	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142165800-142168000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:142167200-142168800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:142167200-142168800	Weak transcription	Left Ventricle	heart
4	chr3:142167200-142169000	Weak transcription	Spleen	Spleen
5	chr3:142167200-142169200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:142167200-142169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:142167200-142174800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:142167200-142174800	Weak transcription	Lung	lung
9	chr3:142167200-142176800	Weak transcription	Gastric	stomach
10	chr3:142167200-142178800	Weak transcription	Small Intestine	intestine
11	chr3:142167200-142187600	Weak transcription	Esophagus	oesophagus
12	chr3:142167200-142192400	Weak transcription	Pancreas	Pancrea
13	chr3:142167400-142168000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:142167400-142169000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:142167400-142169000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:142167400-142169200	Weak transcription	Aorta	Aorta
17	chr3:142167400-142169600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:142167400-142171000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:142167400-142175600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:142167400-142176400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:142167400-142176800	Weak transcription	Placenta	Placenta
22	chr3:142167400-142179600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:142167400-142199400	Weak transcription	Colonic Mucosa	Colon
24	chr3:142167400-142199600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
26	chr3:142167600-142168000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:142167600-142168000	Enhancers	Primary T cells from cord blood	blood
28	chr3:142167600-142168000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:142167600-142168000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr3:142167600-142168000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:142167600-142168000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr3:142167600-142168000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:142167600-142168000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:142167600-142168000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:142167600-142168000	Enhancers	Fetal Kidney	kidney
36	chr3:142167600-142168200	Weak transcription	HMEC	breast
37	chr3:142167600-142168400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:142167600-142168800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:142167600-142169000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:142167600-142169000	Weak transcription	Fetal Thymus	thymus
41	chr3:142167600-142169200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:142167600-142169200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr3:142167600-142169200	Weak transcription	Fetal Heart	heart
44	chr3:142167600-142169400	Weak transcription	Adipose Nuclei	Adipose
45	chr3:142167600-142169600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:142167600-142169600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:142167600-142169800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:142167600-142169800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:142167600-142169800	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:142167600-142169800	Weak transcription	GM12878-XiMat	blood

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