Variant report

Variant	rs9848239
Chromosome Location	chr3:160823488-160823489
allele	A/C
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	GABPA	chr3:160822071-160823714	MCF-7	breast:	n/a	n/a
2	MAX	chr3:160822234-160823527	HCT-116	colon:	n/a	n/a
3	ELF1	chr3:160822220-160823507	MCF-7	breast:	n/a	chr3:160823439-160823450
4	MAX	chr3:160822320-160823501	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr3:160821640-160823909	MCF-7	breast:	n/a	n/a
6	HA-E2F1	chr3:160822200-160823635	MCF-7	breast:	n/a	chr3:160823207-160823221 chr3:160823210-160823224 chr3:160822776-160822788
7	E2F6	chr3:160822061-160823742	H1-hESC	embryonic stem cell:	n/a	chr3:160823207-160823221 chr3:160823210-160823224 chr3:160822776-160822788
8	HDAC2	chr3:160821953-160823716	MCF-7	breast:	n/a	n/a
9	E2F6	chr3:160822343-160823545	H1-hESC	embryonic stem cell:	n/a	chr3:160823207-160823221 chr3:160823210-160823224 chr3:160822776-160822788
10	CTCF	chr3:160823340-160823490	GM12869	blood:	n/a	n/a
11	MAX	chr3:160822306-160823567	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr3:160822372-160823507	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
2	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:
3	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:

Variant related genes	Relation type
B3GALNT1	TF binding region
ENSG00000271052	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1026572	0.85[EUR][1000 genomes]
rs1037888	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936223	0.84[EUR][1000 genomes]
rs12493960	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12631850	0.85[EUR][1000 genomes]
rs13066683	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1599374	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1599376	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1599378	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1599379	0.87[EUR][1000 genomes]
rs1599381	0.90[EUR][1000 genomes]
rs1599383	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1599386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599389	0.90[EUR][1000 genomes]
rs1599390	0.90[EUR][1000 genomes]
rs1609688	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1610158	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2306061	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2404340	0.80[ASN][1000 genomes]
rs2593812	0.93[ASN][1000 genomes]
rs3849524	0.80[ASN][1000 genomes]
rs4273380	0.80[ASN][1000 genomes]
rs4342141	0.81[EUR][1000 genomes]
rs4370045	0.80[ASN][1000 genomes]
rs4414866	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4557202	0.90[EUR][1000 genomes]
rs4597724	0.80[ASN][1000 genomes]
rs4616689	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5004752	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6441354	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6441373	0.80[ASN][1000 genomes]
rs6762645	0.80[ASN][1000 genomes]
rs6765269	0.80[ASN][1000 genomes]
rs6765270	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6769642	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772578	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6774635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775627	0.80[ASN][1000 genomes]
rs6778254	0.82[EUR][1000 genomes]
rs6783085	0.90[EUR][1000 genomes]
rs6789244	0.90[EUR][1000 genomes]
rs6799130	0.90[EUR][1000 genomes]
rs7614375	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7615592	0.80[ASN][1000 genomes]
rs7617204	0.90[EUR][1000 genomes]
rs7619011	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7622047	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623206	0.80[ASN][1000 genomes]
rs7625363	0.89[EUR][1000 genomes]
rs7628880	0.80[AMR][1000 genomes]
rs7629987	0.80[ASN][1000 genomes]
rs7630674	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7630768	0.90[EUR][1000 genomes]
rs7633857	0.90[EUR][1000 genomes]
rs7637086	0.90[EUR][1000 genomes]
rs7647285	0.90[EUR][1000 genomes]
rs7647327	0.80[ASN][1000 genomes]
rs7650703	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7651087	0.90[EUR][1000 genomes]
rs7653361	0.80[ASN][1000 genomes]
rs778642	0.93[ASN][1000 genomes]
rs778643	0.93[ASN][1000 genomes]
rs778645	0.80[ASN][1000 genomes]
rs778646	0.93[ASN][1000 genomes]
rs778649	0.93[ASN][1000 genomes]
rs778654	0.93[ASN][1000 genomes]
rs778663	0.81[AMR][1000 genomes]
rs796609	0.93[ASN][1000 genomes]
rs898680	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898681	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9290065	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290069	0.82[EUR][1000 genomes]
rs9290074	0.80[ASN][1000 genomes]
rs975323	0.80[ASN][1000 genomes]
rs980975	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980976	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820825	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9831488	1.00[ASN][1000 genomes]
rs9846756	0.80[ASN][1000 genomes]
rs9847866	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860360	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9867582	0.87[EUR][1000 genomes]
rs9870059	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv877705	chr3:160818188-160836006	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877706	chr3:160820175-160826404	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877707	chr3:160820175-160836006	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3420135	chr3:160821883-160824431	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv877708	chr3:160821969-160826404	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv877709	chr3:160822198-160826404	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160821800-160823600	Active TSS	Brain Cingulate Gyrus	brain
2	chr3:160821800-160823600	Active TSS	Fetal Brain Female	brain
3	chr3:160821800-160823600	Active TSS	Stomach Smooth Muscle	stomach
4	chr3:160821800-160823800	Active TSS	Brain Substantia Nigra	brain
5	chr3:160821800-160824200	Active TSS	Fetal Kidney	kidney
6	chr3:160822000-160823600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr3:160822000-160823600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr3:160822000-160823600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:160822000-160823600	Active TSS	Brain Angular Gyrus	brain
10	chr3:160822000-160823600	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr3:160822000-160823600	Active TSS	Fetal Brain Male	brain
12	chr3:160822000-160823600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr3:160822000-160823600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr3:160822000-160823600	Active TSS	NHLF	lung
15	chr3:160822000-160823800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:160822000-160823800	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr3:160822200-160823600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:160822200-160823800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:160822200-160823800	Active TSS	Fetal Lung	lung
20	chr3:160822400-160823600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr3:160822400-160823600	Active TSS	Colon Smooth Muscle	Colon
22	chr3:160822400-160823600	Active TSS	Duodenum Mucosa	Duodenum
23	chr3:160822400-160823600	Active TSS	Rectal Smooth Muscle	rectum
24	chr3:160822400-160823800	Active TSS	NHEK	skin
25	chr3:160822800-160823800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
26	chr3:160822800-160824000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr3:160823000-160823600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
28	chr3:160823200-160823600	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr3:160823200-160823600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:160823200-160823600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:160823200-160823600	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr3:160823200-160823600	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr3:160823200-160823600	Flanking Active TSS	Placenta	Placenta
34	chr3:160823200-160823600	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr3:160823200-160823600	Flanking Active TSS	Right Ventricle	heart
36	chr3:160823200-160823600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr3:160823200-160823600	Flanking Active TSS	GM12878-XiMat	blood
38	chr3:160823200-160823600	Flanking Active TSS	HUVEC	blood vessel
39	chr3:160823200-160823600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
40	chr3:160823200-160823600	Flanking Active TSS	Osteobl	bone
41	chr3:160823200-160823800	Flanking Active TSS	Ovary	ovary
42	chr3:160823200-160823800	Flanking Active TSS	NHDF-Ad	bronchial
43	chr3:160823200-160832800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:160823400-160823600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
45	chr3:160823400-160823600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:160823400-160823600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr3:160823400-160823600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
48	chr3:160823400-160823600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
49	chr3:160823400-160823600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr3:160823400-160823600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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