Variant report

Variant	rs13340118
Chromosome Location	chr3:177399416-177399417
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	CTCF	chr3:177399320-177399470	GM12869	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:177398506..177400476-chr3:177405856..177408346,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228561	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10513748	0.89[ASN][1000 genomes]
rs10513749	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10513750	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10936953	0.83[ASN][1000 genomes]
rs10936954	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12487312	0.82[ASN][1000 genomes]
rs12487458	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489304	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489969	0.83[ASN][1000 genomes]
rs12490852	0.81[EUR][1000 genomes]
rs13059117	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13059514	0.83[ASN][1000 genomes]
rs13060224	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060502	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071785	0.82[ASN][1000 genomes]
rs13082519	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097723	0.83[ASN][1000 genomes]
rs13340167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13340172	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499810	0.85[ASN][1000 genomes]
rs1500047	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1604032	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1846628	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2062499	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2062500	0.82[ASN][1000 genomes]
rs28700961	0.81[ASN][1000 genomes]
rs28711160	0.81[ASN][1000 genomes]
rs33964414	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34188001	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34491022	0.82[ASN][1000 genomes]
rs34992356	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35791913	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35847814	0.82[ASN][1000 genomes]
rs35868955	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4857725	0.83[ASN][1000 genomes]
rs4857726	0.83[ASN][1000 genomes]
rs56005554	0.83[ASN][1000 genomes]
rs57405296	1.00[ASN][1000 genomes]
rs62283347	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6443481	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6443482	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6765836	0.83[ASN][1000 genomes]
rs6772134	0.81[ASN][1000 genomes]
rs6779492	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6793629	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793647	0.81[ASN][1000 genomes]
rs6798785	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6803889	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68151580	0.82[ASN][1000 genomes]
rs7610506	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7615900	0.86[ASN][1000 genomes]
rs7639373	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641099	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644248	0.81[ASN][1000 genomes]
rs7646117	0.86[ASN][1000 genomes]
rs7652174	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs937507	0.89[ASN][1000 genomes]
rs937561	0.85[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	esv2752972	chr3:176924298-177425298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177392000-177405400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:177392200-177404400	Weak transcription	Ovary	ovary
3	chr3:177392400-177418800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:177392600-177399600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:177394000-177401000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:177394800-177404800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:177395000-177406000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:177395000-177411600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:177395200-177399600	Weak transcription	Stomach Mucosa	stomach
10	chr3:177395200-177400200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:177395400-177399600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:177395400-177400200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:177396000-177401000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:177396000-177401200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:177396600-177400600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:177396800-177400800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:177397400-177399800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:177397800-177399600	Enhancers	Hela-S3	cervix
19	chr3:177397800-177400200	Weak transcription	Fetal Thymus	thymus
20	chr3:177398000-177400200	Weak transcription	Dnd41	blood
21	chr3:177398000-177400400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:177398000-177400800	Weak transcription	Left Ventricle	heart
23	chr3:177398000-177401200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:177398000-177401400	Weak transcription	Adipose Nuclei	Adipose
25	chr3:177398000-177401800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:177398000-177402000	Enhancers	HUVEC	blood vessel
27	chr3:177398200-177399600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:177398200-177399600	Weak transcription	Right Atrium	heart
29	chr3:177398200-177400400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:177398600-177399800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:177398600-177400400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:177398800-177399600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:177398800-177399600	Weak transcription	Fetal Lung	lung
34	chr3:177398800-177399600	Weak transcription	Spleen	Spleen
35	chr3:177398800-177400200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:177398800-177405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:177398800-177421600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:177399000-177400600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:177399200-177400000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:177399400-177401800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:177399400-177402000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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