Variant report

Variant	rs35496780
Chromosome Location	chr3:28292321-28292322
allele	A/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	EBF1	chr3:28292138-28292861	GM12878	blood:	n/a	chr3:28292787-28292798

No.	Distal block	Cell Line	Cell type
1	chr3:28282408..28284595-chr3:28291176..28293436,3	MCF-7	breast:
2	chr3:28291406..28295098-chr3:28302322..28306116,3	MCF-7	breast:
3	chr3:28291993..28293537-chr3:28308366..28309970,2	K562	blood:

Variant related genes	Relation type
CMC1	TF binding region
ENSG00000187118	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11706332	0.86[ASN][1000 genomes]
rs11708424	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12107256	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13085245	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090296	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13092618	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13093242	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099152	0.89[ASN][1000 genomes]
rs1599826	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1606386	0.90[ASN][1000 genomes]
rs1606388	0.85[ASN][1000 genomes]
rs1610238	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17021221	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17021306	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17638742	0.89[ASN][1000 genomes]
rs17638782	0.89[ASN][1000 genomes]
rs17638991	0.88[ASN][1000 genomes]
rs17695765	0.85[ASN][1000 genomes]
rs2016948	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34017994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34419916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34541614	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34574968	0.88[ASN][1000 genomes]
rs34681294	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34748842	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35217335	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35232922	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35439056	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35460328	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35530532	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35565264	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35575798	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35678778	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35736614	0.89[ASN][1000 genomes]
rs35768817	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35845822	0.89[ASN][1000 genomes]
rs35937120	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4522735	0.89[ASN][1000 genomes]
rs56946005	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62251105	0.88[ASN][1000 genomes]
rs62251108	0.85[ASN][1000 genomes]
rs62252069	0.89[ASN][1000 genomes]
rs66502736	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66716911	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67023418	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68097246	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71087683	0.89[ASN][1000 genomes]
rs7635383	0.90[ASN][1000 genomes]
rs7650831	0.84[ASN][1000 genomes]
rs952888	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28283800-28311400	Weak transcription	Lung	lung
2	chr3:28284000-28304800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:28284000-28309600	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:28284000-28313800	Weak transcription	Ovary	ovary
5	chr3:28284000-28317200	Weak transcription	Gastric	stomach
6	chr3:28284200-28292600	Weak transcription	Psoas Muscle	Psoas
7	chr3:28284200-28292800	Weak transcription	Small Intestine	intestine
8	chr3:28284400-28293600	Weak transcription	Right Ventricle	heart
9	chr3:28284400-28305400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:28284400-28305800	Weak transcription	Hela-S3	cervix
11	chr3:28284400-28311000	Weak transcription	Fetal Intestine Small	intestine
12	chr3:28284400-28312600	Weak transcription	Fetal Lung	lung
13	chr3:28284400-28321800	Weak transcription	NHLF	lung
14	chr3:28284600-28292400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:28284600-28293400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:28284600-28305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:28284600-28306000	Weak transcription	A549	lung
18	chr3:28284600-28307200	Weak transcription	Fetal Intestine Large	intestine
19	chr3:28284600-28311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:28285200-28305200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:28285200-28305600	Weak transcription	Fetal Thymus	thymus
22	chr3:28285400-28294000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:28285600-28315400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:28285800-28305400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:28285800-28311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:28286000-28292600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:28286000-28294000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:28286000-28306000	Weak transcription	K562	blood
29	chr3:28286000-28307200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:28286200-28294400	Weak transcription	Spleen	Spleen
31	chr3:28287200-28304800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:28287600-28317000	Weak transcription	Pancreas	Pancrea
33	chr3:28288000-28293200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr3:28288200-28293600	Weak transcription	HepG2	liver
35	chr3:28288600-28293800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:28288600-28305200	Weak transcription	Liver	Liver
37	chr3:28288600-28311200	Weak transcription	Esophagus	oesophagus
38	chr3:28289000-28292600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:28289200-28292600	Weak transcription	Left Ventricle	heart
40	chr3:28289200-28293200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:28289200-28293400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:28289200-28293600	Weak transcription	Right Atrium	heart
43	chr3:28289400-28292400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:28289400-28292400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:28289400-28305200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:28289400-28305200	Weak transcription	Dnd41	blood
47	chr3:28290000-28292400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:28290200-28293600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:28291000-28293200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:28291000-28293600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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