Variant report

Variant	rs1376676
Chromosome Location	chr1:149871065-149871066
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	E2F6	chr1:149870911-149872042	A549	lung:	n/a	n/a
2	MYC	chr1:149870927-149872011	MCF-7	breast:	n/a	chr1:149871074-149871089 chr1:149871076-149871086 chr1:149871075-149871085 chr1:149871071-149871090 chr1:149871076-149871085
3	SREBP1	chr1:149870634-149871758	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:149870866-149871588	SK-N-MC	brain:	n/a	n/a
5	USF1	chr1:149870786-149871327	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:149870908-149871458	H1-neurons	neurons:	n/a	n/a
7	ZNF263	chr1:149870915-149871463	HEK293-T-REx	kidney:	n/a	n/a
8	ELF1	chr1:149870883-149871308	A549	lung:	n/a	n/a
9	USF1	chr1:149870907-149871331	K562	blood:	n/a	n/a
10	YY1	chr1:149870929-149871790	SK-N-SH	brain:	n/a	n/a
11	SIX5	chr1:149870854-149871376	GM12878	blood:	n/a	chr1:149871047-149871061 chr1:149871049-149871058 chr1:149871051-149871060
12	MAX	chr1:149870903-149871478	Hela-S3	cervix:	n/a	chr1:149871074-149871089 chr1:149871076-149871086 chr1:149871075-149871085 chr1:149871071-149871090 chr1:149871076-149871085
13	TAF1	chr1:149870891-149871572	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr1:149870991-149871174	K562	blood:	n/a	chr1:149871074-149871089 chr1:149871076-149871086 chr1:149871075-149871085 chr1:149871071-149871090 chr1:149871076-149871085
15	POLR2A	chr1:149870891-149872007	MCF-7	breast:	n/a	n/a
16	CTCF	chr1:149871056-149871142	Spleen_OC	spleen:	n/a	n/a
17	STAT3	chr1:149871025-149871378	MCF10A-Er-Src	breast:	n/a	n/a
18	FOXA2	chr1:149870953-149871774	A549	lung:	n/a	n/a
19	POLR2A	chr1:149870921-149871504	GM12891	blood:	n/a	n/a
20	YY1	chr1:149870976-149871233	HCT-116	colon:	n/a	n/a
21	MAZ	chr1:149870833-149871502	GM12878	blood:	n/a	chr1:149871074-149871089 chr1:149871076-149871086 chr1:149871075-149871085 chr1:149871071-149871090 chr1:149871076-149871085
22	POLR2A	chr1:149871004-149871658	GM18951	blood:	n/a	n/a
23	POLR2A	chr1:149871015-149871716	HEK293	kidney:	n/a	n/a
24	POLR2A	chr1:149870897-149871769	SK-N-SH	brain:	n/a	n/a
25	MAX	chr1:149870886-149872106	SK-N-SH	brain:	n/a	chr1:149871074-149871089 chr1:149871076-149871086 chr1:149871075-149871085 chr1:149871071-149871090 chr1:149871076-149871085
26	YY1	chr1:149870855-149871266	K562	blood:	n/a	n/a
27	YY1	chr1:149870956-149871777	GM12878	blood:	n/a	n/a
28	NR2C2	chr1:149870669-149871348	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr1:149870925-149871586	H1-neurons	neurons:	n/a	n/a
30	HCFC1	chr1:149870893-149871288	K562	blood:	n/a	n/a
31	HEY1	chr1:149870988-149871411	HepG2	liver:	n/a	chr1:149871232-149871247
32	CHD2	chr1:149870881-149871826	GM12878	blood:	n/a	n/a
33	SP1	chr1:149870771-149871728	A549	lung:	n/a	chr1:149871428-149871435 chr1:149871431-149871440
34	ATF3	chr1:149870906-149871318	H1-hESC	embryonic stem cell:	n/a	n/a
35	ATF3	chr1:149870754-149871311	HepG2	liver:	n/a	n/a
36	MYC	chr1:149870922-149871322	MCF10A-Er-Src	breast:	n/a	chr1:149871074-149871089 chr1:149871076-149871086 chr1:149871075-149871085 chr1:149871071-149871090 chr1:149871076-149871085
37	POLR2A	chr1:149870934-149871877	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr1:149870880-149871690	PANC-1	pancreas:	n/a	n/a
39	USF2	chr1:149870882-149871265	HepG2	liver:	n/a	n/a
40	NRF1	chr1:149870963-149871350	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr1:149870914-149871407	MCF10A-Er-Src	breast:	n/a	chr1:149871074-149871089 chr1:149871076-149871086 chr1:149871075-149871085 chr1:149871071-149871090 chr1:149871076-149871085
42	E2F6	chr1:149870975-149872044	H1-hESC	embryonic stem cell:	n/a	n/a
43	TAF1	chr1:149870950-149871328	HepG2	liver:	n/a	n/a
44	GABPA	chr1:149870969-149871242	HepG2	liver:	n/a	n/a
45	YY1	chr1:149870911-149871848	SK-N-SH_RA	brain:	n/a	n/a
46	POLR2A	chr1:149870834-149871876	HUVEC	blood vessel:	n/a	n/a
47	YY1	chr1:149870886-149871359	H1-hESC	embryonic stem cell:	n/a	n/a
48	TAF1	chr1:149870957-149871294	GM12891	blood:	n/a	n/a
49	GABPA	chr1:149870847-149871321	A549	lung:	n/a	n/a
50	POLR2A	chr1:149870886-149872077	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:149870476..149872872-chr1:149980684..149982893,3	MCF-7	breast:
2	chr1:149870500..149872892-chr1:150205749..150208479,2	MCF-7	breast:
3	chr1:149870908..149871620-chr7:26903800..26904471,2	Hela-S3	cervix:
4	chr1:149870325..149872593-chr1:150038343..150041327,5	MCF-7	breast:
5	chr1:149869289..149872659-chr1:150292468..150294685,3	MCF-7	breast:
6	chr1:149871037..149872618-chr11:65265092..65267931,2	MCF-7	breast:

Variant related genes	Relation type
BOLA1	TF binding region
ENSG00000143401	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000005020	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000270117	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1044808	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1046332	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs10494261	1.00[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs10494363	1.00[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs10888479	1.00[CHB][hapmap]
rs11205307	0.84[EUR][1000 genomes]
rs11205308	1.00[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs12060830	1.00[GIH][hapmap]
rs12062387	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12077623	0.84[EUR][1000 genomes]
rs12078573	0.81[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs12081082	0.84[EUR][1000 genomes]
rs1349532	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1376675	1.00[EUR][1000 genomes]
rs1451641	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs15931	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs16835135	0.90[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs16836630	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs17643644	0.81[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs1804775	0.87[EUR][1000 genomes]
rs2044891	0.84[EUR][1000 genomes]
rs2198194	0.84[EUR][1000 genomes]
rs3106121	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs35230744	0.84[EUR][1000 genomes]
rs41264630	0.90[EUR][1000 genomes]
rs41265185	0.84[EUR][1000 genomes]
rs41302101	0.84[EUR][1000 genomes]
rs45548131	0.89[EUR][1000 genomes]
rs55633017	1.00[EUR][1000 genomes]
rs55664407	1.00[EUR][1000 genomes]
rs55705001	0.89[EUR][1000 genomes]
rs55885412	0.99[EUR][1000 genomes]
rs56119131	1.00[EUR][1000 genomes]
rs56139516	1.00[EUR][1000 genomes]
rs56229803	1.00[EUR][1000 genomes]
rs56265028	0.91[EUR][1000 genomes]
rs61355654	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6587680	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs68002561	0.86[EUR][1000 genomes]
rs68144650	0.89[EUR][1000 genomes]
rs72692803	0.90[EUR][1000 genomes]
rs72692804	0.89[EUR][1000 genomes]
rs72692805	0.89[EUR][1000 genomes]
rs72692807	0.89[EUR][1000 genomes]
rs72692808	0.89[EUR][1000 genomes]
rs72692810	0.89[EUR][1000 genomes]
rs72692811	0.89[EUR][1000 genomes]
rs72692812	0.89[EUR][1000 genomes]
rs72692813	0.87[EUR][1000 genomes]
rs72692814	0.87[EUR][1000 genomes]
rs72692816	0.87[EUR][1000 genomes]
rs72692818	0.87[EUR][1000 genomes]
rs72692819	0.87[EUR][1000 genomes]
rs72708145	0.90[EUR][1000 genomes]
rs72708148	0.99[EUR][1000 genomes]
rs72708149	0.99[EUR][1000 genomes]
rs72708150	0.99[EUR][1000 genomes]
rs72708151	1.00[EUR][1000 genomes]
rs72708152	1.00[EUR][1000 genomes]
rs72708153	1.00[EUR][1000 genomes]
rs72708157	1.00[EUR][1000 genomes]
rs72708158	0.97[EUR][1000 genomes]
rs72708162	0.91[EUR][1000 genomes]
rs73008195	0.84[EUR][1000 genomes]
rs7524797	0.97[EUR][1000 genomes]
rs7544531	0.90[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap]

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	nsv432820	chr1:148921404-149920927	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	784 gene(s)	inside rSNPs	diseases
2	nsv831525	chr1:149701537-149878033	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
3	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149860800-149871200	Weak transcription	Right Atrium	heart
2	chr1:149870600-149871200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr1:149870600-149871200	Enhancers	Fetal Brain Male	brain
4	chr1:149870600-149871600	Active TSS	GM12878-XiMat	blood
5	chr1:149870800-149871200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:149870800-149871200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr1:149870800-149871200	Enhancers	Fetal Heart	heart
8	chr1:149870800-149871400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:149870800-149871400	Active TSS	Primary hematopoietic stem cells	blood
10	chr1:149870800-149871400	Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr1:149870800-149871400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:149870800-149871600	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr1:149870800-149871600	Active TSS	Liver	Liver
14	chr1:149870800-149871600	Active TSS	Fetal Lung	lung
15	chr1:149870800-149871600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:149870800-149871600	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr1:149870800-149871600	Active TSS	Sigmoid Colon	Sigmoid Colon
18	chr1:149870800-149871800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:149870800-149871800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:149870800-149871800	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr1:149870800-149871800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:149870800-149871800	Active TSS	Brain Hippocampus Middle	brain
23	chr1:149870800-149871800	Active TSS	HepG2	liver
24	chr1:149870800-149872000	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr1:149870800-149872000	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:149870800-149872000	Active TSS	Osteobl	bone
27	chr1:149870800-149872400	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr1:149870800-149872600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr1:149871000-149871200	Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr1:149871000-149871200	Active TSS	Primary B cells from cord blood	blood
31	chr1:149871000-149871200	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr1:149871000-149871200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:149871000-149871200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:149871000-149871200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:149871000-149871200	Active TSS	Muscle Satellite Cultured Cells	--
36	chr1:149871000-149871200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:149871000-149871200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:149871000-149871200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:149871000-149871200	Active TSS	Duodenum Mucosa	Duodenum
40	chr1:149871000-149871200	Active TSS	Fetal Muscle Trunk	muscle
41	chr1:149871000-149871200	Active TSS	Dnd41	blood
42	chr1:149871000-149871200	Active TSS	HUVEC	blood vessel
43	chr1:149871000-149871200	Active TSS	NH-A	brain
44	chr1:149871000-149871400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:149871000-149871400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr1:149871000-149871400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:149871000-149871400	Active TSS	Primary monocytes fromperipheralblood	blood
48	chr1:149871000-149871400	Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr1:149871000-149871400	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr1:149871000-149871400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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