Variant report

Variant	rs1708384
Chromosome Location	chr3:133096031-133096032
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	CTCF	chr3:133095647-133096716	A549	lung:	n/a	chr3:133096424-133096440
2	SMC3	chr3:133094649-133096816	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr3:133095593-133096058	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr3:133095612-133096641	HCT-116	colon:	n/a	n/a
5	RAD21	chr3:133093971-133097201	SK-N-SH	brain:	n/a	chr3:133097180-133097193
6	CTCF	chr3:133095592-133097067	SK-N-SH	brain:	n/a	chr3:133096424-133096440
7	MXI1	chr3:133095106-133096718	SK-N-SH	brain:	n/a	n/a
8	RAD21	chr3:133095504-133096714	HCT-116	colon:	n/a	n/a
9	CTCF	chr3:133095669-133096032	GM12878	blood:	n/a	n/a
10	MAX	chr3:133095702-133096109	HCT-116	colon:	n/a	n/a
11	MYC	chr3:133095706-133096075	K562	blood:	n/a	n/a
12	CTCF	chr3:133095632-133096679	HCT-116	colon:	n/a	chr3:133096424-133096440
13	CTCF	chr3:133095663-133096597	K562	blood:	n/a	chr3:133096424-133096440
14	BHLHE40	chr3:133095739-133096037	K562	blood:	n/a	n/a
15	MAX	chr3:133095728-133096580	NB4	blood:	n/a	n/a
16	RAD21	chr3:133095565-133096117	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr3:133095652-133096639	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr3:133095731-133096056	K562	blood:	n/a	n/a
19	MYC	chr3:133095713-133096032	K562	blood:	n/a	n/a
20	RAD21	chr3:133095623-133096046	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:132757025..132759537-chr3:133094667..133096708,2	MCF-7	breast:
2	chr3:132759646..132760977-chr3:133095922..133096948,16	MCF-7	breast:
3	chr3:132449649..132450503-chr3:133095953..133096664,2	MCF-7	breast:
4	chr3:132760042..132760682-chr3:133095985..133096715,2	K562	blood:
5	chr3:132759827..132760745-chr3:133095936..133096883,3	MCF-7	breast:

Variant related genes	Relation type
TMEM108	TF binding region
ENSG00000144868	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1114630	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1197287	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1197288	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1197293	0.84[ASN][1000 genomes]
rs1197296	0.97[ASN][1000 genomes]
rs1197297	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1197298	1.00[ASN][1000 genomes]
rs1197299	0.99[ASN][1000 genomes]
rs1197301	0.89[ASN][1000 genomes]
rs1197302	0.92[ASN][1000 genomes]
rs1197304	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1197305	1.00[ASN][1000 genomes]
rs1197306	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1197309	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1197313	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1197314	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1201671	0.93[ASN][1000 genomes]
rs1201673	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12631678	0.92[ASN][1000 genomes]
rs1619552	0.96[ASN][1000 genomes]
rs1619622	0.96[ASN][1000 genomes]
rs1708376	0.96[ASN][1000 genomes]
rs1708377	0.93[ASN][1000 genomes]
rs1708385	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1795104	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1795107	1.00[ASN][1000 genomes]
rs2089987	0.90[ASN][1000 genomes]
rs2670179	0.93[ASN][1000 genomes]
rs2699880	0.88[ASN][1000 genomes]
rs2699882	0.93[ASN][1000 genomes]
rs3732572	0.92[ASN][1000 genomes]
rs4854583	0.90[ASN][1000 genomes]
rs4854719	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4854720	0.90[ASN][1000 genomes]
rs56181416	0.86[ASN][1000 genomes]
rs6780144	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6802663	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs938231	0.86[ASN][1000 genomes]
rs9850193	0.90[ASN][1000 genomes]
rs9853752	0.95[ASN][1000 genomes]
rs9853757	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877503	chr3:133035774-133104631	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133080800-133098600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:133083200-133099200	Weak transcription	Lung	lung
3	chr3:133092400-133096400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:133092600-133096400	Enhancers	Fetal Brain Male	brain
5	chr3:133093000-133102400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:133093800-133096400	Enhancers	Fetal Brain Female	brain
7	chr3:133093800-133098200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:133094000-133099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:133094000-133099800	Weak transcription	HSMMtube	muscle
10	chr3:133094000-133109000	Weak transcription	HSMM	muscle
11	chr3:133094200-133100000	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:133094400-133096200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:133094400-133100000	Weak transcription	Brain Angular Gyrus	brain
14	chr3:133094400-133102800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:133094800-133102000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:133094800-133110400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:133095000-133096400	Enhancers	Fetal Stomach	stomach
18	chr3:133095000-133099600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:133095200-133103200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:133095400-133098800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:133095600-133096200	Weak transcription	Fetal Lung	lung
22	chr3:133095800-133096200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:133095800-133096400	Enhancers	Adipose Nuclei	Adipose
24	chr3:133095800-133096400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr3:133095800-133099200	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:133095800-133103200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:133096000-133098200	Weak transcription	Brain Germinal Matrix	brain
28	chr3:133096000-133107800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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