Variant report

Variant	rs9861744
Chromosome Location	chr3:53168113-53168114
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
2	chr3:53163343..53166728-chr3:53167224..53170479,4	MCF-7	breast:
3	chr3:53167017..53169952-chr3:53191720..53194469,2	K562	blood:

Variant related genes	Relation type
ENSG00000163933	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1004807	0.83[ASN][1000 genomes]
rs11130341	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12630819	0.82[EUR][1000 genomes]
rs12638996	0.81[EUR][1000 genomes]
rs13319872	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13433700	0.81[EUR][1000 genomes]
rs1560332	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2253675	0.82[ASN][1000 genomes]
rs2336724	0.82[ASN][1000 genomes]
rs2564922	0.84[ASN][1000 genomes]
rs2564944	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28501212	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28734933	0.83[EUR][1000 genomes]
rs3796351	0.81[EUR][1000 genomes]
rs4282053	0.80[EUR][1000 genomes]
rs4687570	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57261253	0.89[EUR][1000 genomes]
rs57514626	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61296683	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6445565	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6445566	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6769931	0.82[EUR][1000 genomes]
rs6769944	0.82[EUR][1000 genomes]
rs6777975	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783748	0.82[EUR][1000 genomes]
rs6784207	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6792345	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6792363	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6799837	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6809973	0.82[EUR][1000 genomes]
rs73088322	0.80[EUR][1000 genomes]
rs73088327	0.80[EUR][1000 genomes]
rs73088342	0.82[EUR][1000 genomes]
rs930122	0.82[ASN][1000 genomes]
rs9757079	0.83[EUR][1000 genomes]
rs9817467	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9820125	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9820324	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9824325	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9828221	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9830353	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9834111	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9844531	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9845021	0.97[EUR][1000 genomes]
rs9845352	0.81[EUR][1000 genomes]
rs9858469	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9867023	0.82[EUR][1000 genomes]
rs9867590	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9868263	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9868406	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9872260	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9878875	0.82[EUR][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	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3381848	chr3:53167712-53172310	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9861744	SERBP1P3	cis	Thyroid	GTEx
rs9861744	RFT1	cis	Esophagus Muscularis	GTEx
rs9861744	RFT1	cis	Artery Tibial	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53164800-53170600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:53165000-53168600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:53165000-53169800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:53165000-53176200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:53165000-53176400	Weak transcription	Aorta	Aorta
6	chr3:53165200-53169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:53165400-53168400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:53165400-53168600	Weak transcription	Colonic Mucosa	Colon
9	chr3:53165400-53168600	Weak transcription	Fetal Intestine Large	intestine
10	chr3:53165400-53169000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:53165400-53173800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:53165400-53176000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:53165600-53168400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:53165600-53168400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:53165600-53168400	Weak transcription	Hela-S3	cervix
16	chr3:53165600-53168400	Enhancers	HepG2	liver
17	chr3:53165600-53168600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:53165600-53168600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:53165600-53168600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:53165600-53168600	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:53165600-53168600	Weak transcription	Fetal Lung	lung
22	chr3:53165600-53168600	Weak transcription	Lung	lung
23	chr3:53165600-53168600	Weak transcription	Pancreas	Pancrea
24	chr3:53165600-53168600	Weak transcription	Right Ventricle	heart
25	chr3:53165600-53168600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:53165600-53168800	Weak transcription	Brain Substantia Nigra	brain
27	chr3:53165600-53168800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:53165600-53168800	Weak transcription	Esophagus	oesophagus
29	chr3:53165600-53169200	Weak transcription	Brain Anterior Caudate	brain
30	chr3:53165600-53169600	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:53165600-53170800	Weak transcription	Fetal Thymus	thymus
32	chr3:53165600-53173400	Weak transcription	Gastric	stomach
33	chr3:53165600-53174200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:53165600-53174200	Weak transcription	Fetal Heart	heart
35	chr3:53165600-53174200	Weak transcription	Left Ventricle	heart
36	chr3:53165600-53174600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:53165600-53177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:53165600-53181400	Weak transcription	Spleen	Spleen
39	chr3:53165800-53168400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:53165800-53168600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:53165800-53168600	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:53165800-53170600	Weak transcription	GM12878-XiMat	blood
43	chr3:53165800-53175400	Weak transcription	Placenta	Placenta
44	chr3:53166200-53168200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:53166200-53174600	Weak transcription	Primary B cells from cord blood	blood
46	chr3:53166400-53168600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:53166400-53168600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:53166400-53168600	Weak transcription	Right Atrium	heart
49	chr3:53166400-53170200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:53166400-53171200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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