Variant report

Variant	rs2277876
Chromosome Location	chr2:99797598-99797599
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	TEAD4	chr2:99797117-99798070	K562	blood:	n/a	n/a
2	POLR2A	chr2:99797196-99798040	GM18951	blood:	n/a	n/a
3	ZEB1	chr2:99797191-99797758	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:99797016-99798274	HepG2	liver:	n/a	n/a
5	BCL3	chr2:99797232-99797983	A549	lung:	n/a	n/a
6	RCOR1	chr2:99797239-99798061	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr2:99797256-99798144	H1-neurons	neurons:	n/a	n/a
8	TCF12	chr2:99797064-99798126	ECC-1	luminal epithelium:	n/a	n/a
9	WRNIP1	chr2:99797140-99798374	GM12878	blood:	n/a	n/a
10	MAX	chr2:99797253-99798389	Hela-S3	cervix:	n/a	chr2:99797922-99797931 chr2:99797515-99797524
11	CREB1	chr2:99797241-99798051	GM12878	blood:	n/a	n/a
12	CTCF	chr2:99797434-99797786	GM12878	blood:	n/a	n/a
13	MAX	chr2:99797296-99798142	NB4	blood:	n/a	chr2:99797922-99797931 chr2:99797515-99797524
14	SRF	chr2:99797256-99797964	ECC-1	luminal epithelium:	n/a	n/a
15	MAZ	chr2:99797265-99797958	K562	blood:	n/a	chr2:99797922-99797931 chr2:99797515-99797524
16	SIN3AK20	chr2:99797166-99797798	A549	lung:	n/a	n/a
17	POLR2A	chr2:99797200-99798033	GM19193	blood:	n/a	n/a
18	STAT1	chr2:99797055-99798057	Hela-S3	cervix:	n/a	chr2:99797502-99797511 chr2:99797497-99797517 chr2:99797501-99797512 chr2:99797503-99797511 chr2:99797497-99797517 chr2:99797503-99797512
19	USF1	chr2:99797219-99797997	SK-N-SH_RA	brain:	n/a	n/a
20	MAX	chr2:99796945-99798494	A549	lung:	n/a	chr2:99797922-99797931 chr2:99797515-99797524
21	CEBPB	chr2:99797432-99797926	K562	blood:	n/a	n/a
22	BCLAF1	chr2:99797100-99797897	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:99797224-99798003	A549	lung:	n/a	n/a
24	ZBTB33	chr2:99797288-99797784	A549	lung:	n/a	n/a
25	POLR2A	chr2:99797216-99798267	K562	blood:	n/a	n/a
26	NFYB	chr2:99797465-99798017	K562	blood:	n/a	n/a
27	MAX	chr2:99797335-99798061	K562	blood:	n/a	chr2:99797922-99797931 chr2:99797515-99797524
28	REST	chr2:99797428-99797769	H1-hESC	embryonic stem cell:	n/a	n/a
29	SPI1	chr2:99797278-99798053	HL-60	blood:	n/a	n/a
30	POLR2A	chr2:99797217-99797884	GM12878	blood:	n/a	n/a
31	SIN3AK20	chr2:99797367-99797755	K562	blood:	n/a	n/a
32	STAT3	chr2:99797318-99797977	MCF10A-Er-Src	breast:	n/a	chr2:99797502-99797511 chr2:99797497-99797517 chr2:99797503-99797511 chr2:99797501-99797512 chr2:99797497-99797517 chr2:99797503-99797512
33	SIN3AK20	chr2:99797207-99797893	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr2:99797216-99798042	GM12891	blood:	n/a	n/a
35	CHD2	chr2:99797298-99798238	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr2:99797155-99798009	HUVEC	blood vessel:	n/a	n/a
37	YY1	chr2:99797157-99798068	SK-N-SH	brain:	n/a	n/a
38	MAX	chr2:99797285-99798344	HepG2	liver:	n/a	chr2:99797922-99797931 chr2:99797515-99797524
39	POU2F2	chr2:99797276-99797871	GM12878	blood:	n/a	n/a
40	MYC	chr2:99797579-99797699	MCF-7	breast:	n/a	n/a
41	POLR2A	chr2:99797139-99798085	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr2:99797121-99797958	Raji	blood:	n/a	n/a
43	ELK1	chr2:99797304-99797766	K562	blood:	n/a	n/a
44	ATF3	chr2:99797260-99797798	GM12878	blood:	n/a	chr2:99797515-99797524 chr2:99797515-99797535
45	E2F6	chr2:99797358-99798074	H1-hESC	embryonic stem cell:	n/a	chr2:99797531-99797540
46	POLR2A	chr2:99797202-99798782	K562	blood:	n/a	n/a
47	CREB1	chr2:99797453-99797773	A549	lung:	n/a	n/a
48	REST	chr2:99796988-99798398	H1-neurons	neurons:	n/a	n/a
49	TCF12	chr2:99797420-99797723	H1-hESC	embryonic stem cell:	n/a	n/a
50	TAF1	chr2:99797052-99798226	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99782491..99787778-chr2:99795073..99800536,8	MCF-7	breast:
2	chr2:99756618..99760530-chr2:99796957..99801063,7	MCF-7	breast:
3	chr2:99767297..99778137-chr2:99793643..99800044,16	MCF-7	breast:
4	chr2:99768084..99772423-chr2:99795960..99799744,7	K562	blood:
5	chr2:99792102..99795354-chr2:99796757..99799088,4	MCF-7	breast:
6	chr2:99786426..99788030-chr2:99796073..99799242,3	K562	blood:
7	chr2:99757575..99760395-chr2:99795675..99798209,3	K562	blood:
8	chr2:99767233..99772869-chr2:99793831..99799744,8	K562	blood:
9	chr2:99796217..99799127-chr2:100105224..100108883,4	K562	blood:
10	chr2:99797161..99797680-chr2:99952801..99953346,2	K562	blood:
11	chr2:99769587..99774574-chr2:99795787..99799597,12	MCF-7	breast:
12	chr2:99755178..99760444-chr2:99795813..99800130,7	MCF-7	breast:
13	chr2:99796467..99798602-chr2:99952178..99954116,2	K562	blood:
14	chr12:56551919..56552646-chr2:99797563..99798171,2	Hela-S3	cervix:
15	chr2:99796197..99799811-chr2:99951417..99956311,9	MCF-7	breast:
16	chr2:99796817..99802176-chr2:99802213..99807656,6	MCF-7	breast:
17	chr2:99694874..99697753-chr2:99797016..99799140,2	MCF-7	breast:
18	chr2:99797020..99797886-chr20:34252187..34252957,2	Hela-S3	cervix:
19	chr2:99796217..99798600-chr2:100104908..100107681,3	K562	blood:
20	chr2:99756983..99757661-chr2:99797222..99798184,3	MCF-7	breast:
21	chr2:99796308..99800210-chr2:99949212..99956082,14	MCF-7	breast:

Variant related genes	Relation type
MITD1	TF binding region
MRPL30	TF binding region
ENSG00000273155	Chromatin interaction
ENSG00000135945	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000115514	Chromatin interaction
ENSG00000244462	Chromatin interaction
ENSG00000158417	Chromatin interaction
ENSG00000214078	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000273045	Chromatin interaction
ENSG00000144182	Chromatin interaction
ENSG00000135951	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10496334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496335	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123760	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123768	0.93[EUR][1000 genomes]
rs11526114	0.86[EUR][1000 genomes]
rs12233087	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12620997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1586434	0.86[EUR][1000 genomes]
rs17020569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17022180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs17022249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28785294	1.00[EUR][1000 genomes]
rs28794804	0.83[ASN][1000 genomes]
rs35071324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3791211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4850895	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs56926889	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57273701	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57743480	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58595226	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58635701	0.93[EUR][1000 genomes]
rs58745514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59252741	0.82[ASN][1000 genomes]
rs59506582	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60056452	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60516303	0.83[ASN][1000 genomes]
rs60653099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6719145	0.86[EUR][1000 genomes]
rs6746969	0.86[EUR][1000 genomes]
rs6748497	0.86[EUR][1000 genomes]
rs6749198	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7568749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608938	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs9752510	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2277876	LIPT1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99795200-99798400	Active TSS	GM12878-XiMat	blood
2	chr2:99795400-99798800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:99795600-99799600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:99795800-99798800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr2:99795800-99799200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:99796000-99798600	Active TSS	Muscle Satellite Cultured Cells	--
7	chr2:99796000-99798800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr2:99796000-99798800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:99796000-99799200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:99796400-99798600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr2:99796400-99798800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr2:99796400-99798800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:99796400-99798800	Active TSS	HMEC	breast
14	chr2:99796400-99798800	Active TSS	NHDF-Ad	bronchial
15	chr2:99796400-99799200	Active TSS	A549	lung
16	chr2:99796400-99799400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr2:99796600-99797600	Active TSS	Brain Germinal Matrix	brain
18	chr2:99796600-99798000	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr2:99796600-99798200	Active TSS	Brain Angular Gyrus	brain
20	chr2:99796600-99798200	Active TSS	Fetal Stomach	stomach
21	chr2:99796600-99798400	Active TSS	Brain Anterior Caudate	brain
22	chr2:99796600-99798600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:99796600-99798600	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr2:99796600-99798600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr2:99796600-99798800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:99796600-99798800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:99796600-99798800	Active TSS	Fetal Intestine Large	intestine
28	chr2:99796600-99798800	Active TSS	Fetal Intestine Small	intestine
29	chr2:99796600-99798800	Active TSS	Fetal Kidney	kidney
30	chr2:99796600-99798800	Active TSS	HSMMtube	muscle
31	chr2:99796600-99798800	Active TSS	NH-A	brain
32	chr2:99796600-99799200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:99796600-99799200	Active TSS	Fetal Brain Female	brain
34	chr2:99796800-99797800	Active TSS	Primary monocytes fromperipheralblood	blood
35	chr2:99796800-99797800	Active TSS	Primary T cells fromperipheralblood	blood
36	chr2:99796800-99797800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:99796800-99798000	Active TSS	Primary B cells from peripheral blood	blood
38	chr2:99796800-99798200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:99796800-99798200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr2:99796800-99798200	Active TSS	Brain Hippocampus Middle	brain
41	chr2:99796800-99798200	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr2:99796800-99798200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:99796800-99798200	Active TSS	Colonic Mucosa	Colon
44	chr2:99796800-99798200	Active TSS	Colon Smooth Muscle	Colon
45	chr2:99796800-99798200	Active TSS	Fetal Brain Male	brain
46	chr2:99796800-99798200	Active TSS	Fetal Muscle Leg	muscle
47	chr2:99796800-99798200	Active TSS	Placenta	Placenta
48	chr2:99796800-99798200	Active TSS	Fetal Thymus	thymus
49	chr2:99796800-99798200	Active TSS	Rectal Smooth Muscle	rectum
50	chr2:99796800-99798400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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