Variant report

Variant	rs73983727
Chromosome Location	chr2:209131638-209131639
allele	G/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	MBD4	chr2:209129927-209131651	HepG2	liver:	n/a	n/a
2	TBL1XR1	chr2:209129765-209131669	GM12878	blood:	n/a	n/a
3	MYC	chr2:209131607-209132045	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr2:209129665-209132065	GM12891	blood:	n/a	n/a
5	ZC3H11A	chr2:209131264-209131682	K562	blood:	n/a	n/a
6	POLR2A	chr2:209129898-209131869	GM12878	blood:	n/a	n/a
7	SIN3A	chr2:209130131-209131898	H1-hESC	embryonic stem cell:	n/a	chr2:209131049-209131062
8	MXI1	chr2:209130119-209131935	GM12878	blood:	n/a	n/a
9	MAZ	chr2:209130094-209131810	GM12878	blood:	n/a	chr2:209130353-209130362
10	TBP	chr2:209130057-209131721	GM12878	blood:	n/a	n/a
11	WRNIP1	chr2:209129994-209131685	GM12878	blood:	n/a	n/a
12	MAX	chr2:209130438-209131807	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr2:209130058-209131921	PBDE	blood:	n/a	n/a
14	TAF1	chr2:209130541-209131675	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZKSCAN1	chr2:209130583-209131727	Hela-S3	cervix:	n/a	n/a
16	UBTF	chr2:209130374-209131752	K562	blood:	n/a	n/a
17	FOXA1	chr2:209131625-209132026	HepG2	liver:	n/a	n/a
18	RELA	chr2:209129768-209131704	GM15510	blood:	n/a	n/a
19	POLR2A	chr2:209130030-209131702	HL-60	blood:	n/a	n/a
20	EBF1	chr2:209130262-209131690	GM12878	blood:	n/a	n/a
21	CREB1	chr2:209129932-209131727	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:209130453-209131914	MCF10A-Er-Src	breast:	n/a	n/a
23	CHD2	chr2:209130171-209131701	GM12878	blood:	n/a	n/a
24	SIN3AK20	chr2:209130713-209131649	H1-hESC	embryonic stem cell:	n/a	n/a
25	MXI1	chr2:209129623-209132308	SK-N-SH	brain:	n/a	n/a
26	SMC3	chr2:209131382-209131756	Hela-S3	cervix:	n/a	n/a
27	STAT1	chr2:209130206-209131874	GM12878	blood:	n/a	chr2:209131854-209131863 chr2:209130795-209130806 chr2:209131522-209131533 chr2:209130796-209130805 chr2:209130797-209130806 chr2:209130967-209130979
28	REST	chr2:209130055-209131684	H1-neurons	neurons:	n/a	chr2:209131202-209131220
29	POLR2A	chr2:209130472-209131997	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr2:209130358-209131960	IMR90	lung:	n/a	n/a
31	ZNF263	chr2:209130063-209131661	HEK293-T-REx	kidney:	n/a	chr2:209130901-209130910 chr2:209131183-209131192
32	STAT3	chr2:209131618-209131731	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr2:209131616-209132054	MCF10A-Er-Src	breast:	n/a	chr2:209131820-209131829 chr2:209131664-209131676
34	FOXA1	chr2:209131451-209132110	HepG2	liver:	n/a	n/a
35	CEBPB	chr2:209131486-209131941	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr2:209129769-209132058	GM12878	blood:	n/a	n/a
37	RELA	chr2:209129854-209131977	GM10847	blood:	n/a	n/a
38	MTA3	chr2:209129897-209131927	GM12878	blood:	n/a	n/a
39	POLR2A	chr2:209129967-209131750	GM18951	blood:	n/a	n/a
40	CEBPB	chr2:209131556-209131736	K562	blood:	n/a	n/a
41	MAFK	chr2:209131456-209131997	IMR90	lung:	n/a	n/a
42	EP300	chr2:209130085-209131756	GM12878	blood:	n/a	n/a
43	HCFC1	chr2:209130116-209131803	Hela-S3	cervix:	n/a	n/a
44	KAP1	chr2:209129892-209131658	HEK293	kidney:	n/a	n/a
45	BHLHE40	chr2:209129762-209131735	GM12878	blood:	n/a	n/a
46	KAP1	chr2:209130160-209131856	U2OS	brain:	n/a	n/a
47	POLR2A	chr2:209129897-209131763	K562	blood:	n/a	n/a
48	TBP	chr2:209130246-209131941	Hela-S3	cervix:	n/a	n/a
49	FOXA1	chr2:209131608-209132174	HepG2	liver:	n/a	n/a
50	MXI1	chr2:209130506-209131854	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:209121994..209124234-chr2:209131369..209133621,2	MCF-7	breast:
2	chr2:209104332..209106656-chr2:209130862..209133286,2	MCF-7	breast:
3	chr2:209129671..209132812-chr2:209132994..209136144,5	MCF-7	breast:
4	chr2:209116323..209122695-chr2:209127326..209132568,14	K562	blood:
5	chr2:209116323..209123332-chr2:209127326..209134005,17	K562	blood:
6	chr2:209129669..209131681-chr2:209132251..209135245,2	K562	blood:
7	chr2:209117138..209121626-chr2:209129108..209132782,7	MCF-7	breast:
8	chr2:209118313..209121811-chr2:209130870..209135068,6	MCF-7	breast:

Variant related genes	Relation type
IDH1	TF binding region
ENSG00000231908	Chromatin interaction
ENSG00000138413	Chromatin interaction
ENSG00000228380	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10171006	0.94[ASN][1000 genomes]
rs10173938	0.85[ASN][1000 genomes]
rs10176626	0.88[ASN][1000 genomes]
rs10189031	0.88[ASN][1000 genomes]
rs10197958	0.83[ASN][1000 genomes]
rs10201702	0.94[ASN][1000 genomes]
rs10208004	0.90[ASN][1000 genomes]
rs10804168	0.94[ASN][1000 genomes]
rs10932256	0.94[ASN][1000 genomes]
rs10932259	0.94[ASN][1000 genomes]
rs10932260	0.88[ASN][1000 genomes]
rs11677618	0.90[ASN][1000 genomes]
rs11691208	0.94[ASN][1000 genomes]
rs11691313	0.94[ASN][1000 genomes]
rs12479282	0.90[ASN][1000 genomes]
rs12623816	0.94[ASN][1000 genomes]
rs12694105	0.90[ASN][1000 genomes]
rs1370370	0.94[ASN][1000 genomes]
rs1584200	0.85[ASN][1000 genomes]
rs16840898	0.94[ASN][1000 genomes]
rs16840910	0.94[ASN][1000 genomes]
rs16840936	0.94[ASN][1000 genomes]
rs1900239	0.88[ASN][1000 genomes]
rs2196604	0.85[ASN][1000 genomes]
rs2363466	0.85[ASN][1000 genomes]
rs2885786	0.85[ASN][1000 genomes]
rs4673390	0.90[ASN][1000 genomes]
rs4673391	0.85[ASN][1000 genomes]
rs4673392	0.85[ASN][1000 genomes]
rs4673393	0.88[ASN][1000 genomes]
rs4673395	0.94[ASN][1000 genomes]
rs4675748	0.88[ASN][1000 genomes]
rs4675750	0.94[ASN][1000 genomes]
rs4675751	0.88[ASN][1000 genomes]
rs56154808	0.99[AFR][1000 genomes]
rs57797425	0.94[ASN][1000 genomes]
rs60446438	0.97[ASN][1000 genomes]
rs6435441	0.94[ASN][1000 genomes]
rs6435443	0.94[ASN][1000 genomes]
rs6708926	0.94[ASN][1000 genomes]
rs6711933	0.94[ASN][1000 genomes]
rs6724208	0.88[ASN][1000 genomes]
rs6733607	0.94[ASN][1000 genomes]
rs6736599	0.88[ASN][1000 genomes]
rs6742461	0.94[ASN][1000 genomes]
rs7569723	0.94[ASN][1000 genomes]
rs7574324	0.94[ASN][1000 genomes]
rs7581075	0.94[ASN][1000 genomes]
rs7587752	0.88[ASN][1000 genomes]
rs893256	0.94[ASN][1000 genomes]
rs9283521	0.94[ASN][1000 genomes]
rs9288392	0.88[ASN][1000 genomes]
rs934712	0.94[ASN][1000 genomes]
rs934714	0.94[ASN][1000 genomes]
rs959855	0.94[ASN][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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209129600-209132000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:209129800-209132800	Active TSS	H1 Cell Line	embryonic stem cell
3	chr2:209129800-209132800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:209129800-209133000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:209129800-209133000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:209130000-209131800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:209130000-209132000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr2:209130000-209132200	Active TSS	Aorta	Aorta
9	chr2:209130000-209132200	Active TSS	Right Ventricle	heart
10	chr2:209130000-209132400	Active TSS	Psoas Muscle	Psoas
11	chr2:209130000-209132600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr2:209130000-209132600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:209130000-209132600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:209130000-209132800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr2:209130000-209132800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:209130000-209132800	Active TSS	Ovary	ovary
17	chr2:209130200-209131800	Active TSS	Brain Germinal Matrix	brain
18	chr2:209130200-209131800	Active TSS	Brain Hippocampus Middle	brain
19	chr2:209130200-209131800	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr2:209130200-209131800	Active TSS	Brain Substantia Nigra	brain
21	chr2:209130200-209131800	Active TSS	Gastric	stomach
22	chr2:209130200-209131800	Active TSS	Left Ventricle	heart
23	chr2:209130200-209131800	Active TSS	Placenta Amnion	Placenta Amnion
24	chr2:209130200-209132000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:209130200-209132000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:209130200-209132000	Active TSS	Fetal Muscle Trunk	muscle
27	chr2:209130200-209132000	Bivalent/Poised TSS	HepG2	liver
28	chr2:209130200-209132200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:209130200-209132200	Active TSS	Fetal Intestine Small	intestine
30	chr2:209130200-209132200	Active TSS	A549	lung
31	chr2:209130200-209132400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:209130200-209132400	Active TSS	Fetal Intestine Large	intestine
33	chr2:209130200-209132400	Active TSS	Right Atrium	heart
34	chr2:209130200-209132400	Active TSS	Dnd41	blood
35	chr2:209130200-209132600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:209130200-209132600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:209130200-209132600	Active TSS	Colon Smooth Muscle	Colon
38	chr2:209130200-209132800	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr2:209130200-209132800	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr2:209130200-209132800	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr2:209130200-209133400	Active TSS	K562	blood
42	chr2:209130400-209131800	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr2:209130400-209131800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr2:209130400-209131800	Active TSS	Fetal Heart	heart
45	chr2:209130400-209131800	Active TSS	Fetal Kidney	kidney
46	chr2:209130400-209131800	Active TSS	Fetal Lung	lung
47	chr2:209130400-209131800	Active TSS	Lung	lung
48	chr2:209130400-209131800	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr2:209130400-209131800	Active TSS	Small Intestine	intestine
50	chr2:209130400-209132000	Active TSS	Fetal Muscle Leg	muscle

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