Variant report

Variant	rs1263345
Chromosome Location	chr4:2928125-2928126
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	TCF3	chr4:2927981-2928213	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:2928052-2928210	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:2927989-2928287	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:2927946-2928168	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:2927918-2928235	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:2928044-2928389	HL-60	blood:	n/a	n/a
7	BCL3	chr4:2927983-2928205	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2844628..2846821-chr4:2925950..2928753,2	MCF-7	breast:
2	chr4:2812607..2814330-chr4:2927336..2930211,2	MCF-7	breast:

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000087266	Chromatin interaction
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1012365	0.94[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1242228	0.91[CHB][hapmap]
rs1263338	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1263339	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1263342	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1263344	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1263347	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1263349	0.83[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1263359	0.82[CHB][hapmap]
rs1263360	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs12642795	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1419045	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16843452	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs16843523	0.94[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2051560	0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2071695	0.92[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2097081	0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2185885	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237004	1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2239728	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2282772	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2282773	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2282774	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2285084	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2301374	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857866	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3775068	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs3796469	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4690000	0.94[CEU][hapmap]
rs4690001	0.91[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4690065	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4961	0.94[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4963	0.88[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs762847	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs7664801	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv980393	chr4:2927263-2930956	Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2893200-2932600	Strong transcription	Fetal Thymus	thymus
2	chr4:2901200-2934600	Weak transcription	Hela-S3	cervix
3	chr4:2907400-2935400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:2911200-2935000	Weak transcription	Psoas Muscle	Psoas
5	chr4:2912600-2934800	Weak transcription	A549	lung
6	chr4:2913000-2935000	Weak transcription	K562	blood
7	chr4:2915600-2933000	Weak transcription	Right Atrium	heart
8	chr4:2916400-2929800	Weak transcription	Fetal Heart	heart
9	chr4:2917000-2932000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:2923400-2932000	Strong transcription	Duodenum Mucosa	Duodenum
11	chr4:2923400-2932000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr4:2923800-2933600	Strong transcription	Thymus	Thymus
13	chr4:2924000-2932000	Strong transcription	Fetal Muscle Leg	muscle
14	chr4:2924000-2934400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:2924200-2928200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:2924200-2928800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:2924200-2932000	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:2924200-2932400	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:2924200-2932600	Strong transcription	Rectal Smooth Muscle	rectum
20	chr4:2924200-2932600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:2924200-2932800	Strong transcription	Adipose Nuclei	Adipose
22	chr4:2924200-2933000	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr4:2924200-2934400	Strong transcription	Fetal Stomach	stomach
24	chr4:2924200-2934800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:2924400-2932400	Strong transcription	Ovary	ovary
26	chr4:2924400-2933800	Strong transcription	Fetal Brain Female	brain
27	chr4:2924400-2934200	Strong transcription	Brain Germinal Matrix	brain
28	chr4:2924600-2932000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr4:2924600-2932200	Strong transcription	Left Ventricle	heart
30	chr4:2924600-2932600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:2924800-2930400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:2924800-2931400	Strong transcription	Colonic Mucosa	Colon
33	chr4:2924800-2931600	Strong transcription	HepG2	liver
34	chr4:2924800-2931800	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:2924800-2931800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:2924800-2933600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:2925000-2928800	Strong transcription	Placenta	Placenta
38	chr4:2925000-2931800	Strong transcription	Primary B cells from cord blood	blood
39	chr4:2925000-2932400	Strong transcription	Colon Smooth Muscle	Colon
40	chr4:2925000-2933800	Strong transcription	Dnd41	blood
41	chr4:2925000-2934400	Strong transcription	Osteobl	bone
42	chr4:2925200-2930200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr4:2925200-2932600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr4:2925200-2932600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:2925200-2933200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:2925200-2933400	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr4:2925200-2934800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:2925400-2930800	Weak transcription	Stomach Mucosa	stomach
49	chr4:2925400-2932000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:2925400-2932400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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