Variant report

Variant	rs580978
Chromosome Location	chr1:176175133-176175134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr1:176174648-176175398	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:176175022-176175533	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:176174880-176177672	MCF10A-Er-Src	breast:	n/a	n/a
4	CHD1	chr1:176175055-176177236	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:176175121-176178142	GM12878	blood:	n/a	n/a
6	MXI1	chr1:176174331-176177577	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:176174989-176178000	GM12878	blood:	n/a	n/a
8	UBTF	chr1:176174742-176177096	K562	blood:	n/a	n/a
9	MXI1	chr1:176174817-176177037	Hela-S3	cervix:	n/a	n/a
10	SMARCC1	chr1:176174966-176177413	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr1:176174606-176177275	IMR90	lung:	n/a	n/a
12	ZNF263	chr1:176174822-176177099	HEK293-T-REx	kidney:	n/a	n/a
13	HCFC1	chr1:176174420-176177567	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:176174704-176177271	PBDE	blood:	n/a	n/a
15	POLR2A	chr1:176174335-176179842	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:176103163..176105549-chr1:176174911..176176507,2	MCF-7	breast:
2	chr1:176173011..176175241-chr1:176190207..176192824,3	K562	blood:
3	chr1:176153551..176156175-chr1:176174165..176176640,2	K562	blood:
4	chr1:176152065..176154740-chr1:176172886..176175167,2	MCF-7	breast:
5	chr1:176174633..176176230-chr7:139024705..139027215,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236021	TF binding region
ENSG00000164898	Chromatin interaction
ENSG00000269955	Chromatin interaction
ENSG00000143207	Chromatin interaction
ENSG00000146963	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10494499	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs10798449	0.87[ASN][1000 genomes]
rs10913150	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801582	0.87[ASN][1000 genomes]
rs12403794	0.84[EUR][1000 genomes]
rs16849645	0.92[ASN][1000 genomes]
rs16849697	0.87[ASN][1000 genomes]
rs16849735	1.00[JPT][hapmap]
rs17351808	0.91[CEU][hapmap]
rs17351933	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs17352072	0.91[EUR][1000 genomes]
rs17354252	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs1770643	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1831447	0.81[ASN][1000 genomes]
rs2039231	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[ASN][1000 genomes]
rs2039232	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs2136545	0.87[ASN][1000 genomes]
rs2481627	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2481634	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2481635	0.88[EUR][1000 genomes]
rs2481639	0.81[ASN][1000 genomes]
rs2481641	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2481647	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2481651	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2481653	0.85[CHB][hapmap]
rs2481657	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2502822	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2502824	0.85[CHB][hapmap]
rs2502826	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2502830	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502832	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2502834	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2502835	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2502836	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2502841	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2502842	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2502847	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2861630	0.91[CEU][hapmap]
rs4129061	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4307526	0.90[AMR][1000 genomes]
rs4314844	0.90[AMR][1000 genomes]
rs4460596	0.91[CEU][hapmap]
rs4543747	0.85[CHB][hapmap]
rs4603086	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4650934	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4650938	0.87[ASN][1000 genomes]
rs4652154	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs4652155	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs471534	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs533403	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553852	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs559341	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs56367284	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57395528	0.84[ASN][1000 genomes]
rs58325269	0.81[ASN][1000 genomes]
rs59276566	0.87[ASN][1000 genomes]
rs598177	0.81[ASN][1000 genomes]
rs599326	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs602933	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs60719126	0.86[EUR][1000 genomes]
rs611883	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61821007	0.86[EUR][1000 genomes]
rs61821009	0.86[EUR][1000 genomes]
rs61821028	0.84[EUR][1000 genomes]
rs61821029	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61822662	0.91[EUR][1000 genomes]
rs6684747	0.86[AMR][1000 genomes]
rs6704509	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes]
rs704825	0.81[ASN][1000 genomes]
rs704827	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704830	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs704831	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs704832	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs74127185	0.83[EUR][1000 genomes]
rs7525001	1.00[JPT][hapmap]
rs7536464	0.85[CHB][hapmap]
rs7545639	0.90[AMR][1000 genomes]
rs7554913	0.91[CEU][hapmap]
rs791744	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs791795	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs791800	0.80[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791801	0.91[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs796933	0.85[CHB][hapmap];0.81[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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS 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	33 gene(s)	inside rSNPs	diseases
2	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
2	chr1:176166000-176175400	Weak transcription	Spleen	Spleen
3	chr1:176171600-176175200	Weak transcription	Gastric	stomach
4	chr1:176171600-176175400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:176171800-176175200	Weak transcription	Lung	lung
6	chr1:176173000-176175200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr1:176173000-176175200	Flanking Active TSS	Dnd41	blood
8	chr1:176173400-176175400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr1:176173600-176175800	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr1:176173600-176175800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:176173600-176176000	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr1:176173800-176175400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:176173800-176175800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:176173800-176177600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:176173800-176177600	Active TSS	HSMM	muscle
16	chr1:176174000-176175200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr1:176174000-176175400	Flanking Active TSS	Hela-S3	cervix
18	chr1:176174000-176175600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:176174000-176175800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr1:176174000-176177200	Active TSS	Fetal Intestine Small	intestine
21	chr1:176174000-176177400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:176174000-176177400	Active TSS	Right Ventricle	heart
23	chr1:176174000-176177600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:176174000-176177600	Active TSS	HSMMtube	muscle
25	chr1:176174200-176175200	Weak transcription	Left Ventricle	heart
26	chr1:176174200-176175200	Weak transcription	Pancreas	Pancrea
27	chr1:176174200-176175200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr1:176174200-176175400	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr1:176174200-176175400	Active TSS	HepG2	liver
30	chr1:176174200-176175400	Flanking Active TSS	NHEK	skin
31	chr1:176174200-176175600	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr1:176174200-176175600	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr1:176174200-176175800	Active TSS	Right Atrium	heart
34	chr1:176174200-176177200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:176174200-176177200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:176174200-176177200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:176174200-176177200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:176174200-176177200	Active TSS	Fetal Muscle Leg	muscle
39	chr1:176174200-176177200	Active TSS	Psoas Muscle	Psoas
40	chr1:176174200-176177400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:176174200-176177400	Active TSS	Fetal Intestine Large	intestine
42	chr1:176174200-176177400	Active TSS	Ovary	ovary
43	chr1:176174200-176177600	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr1:176174200-176177600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:176174200-176177800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:176174400-176175200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr1:176174400-176175200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr1:176174400-176175200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr1:176174400-176175200	Flanking Active TSS	Fetal Lung	lung
50	chr1:176174400-176175400	Flanking Active TSS	Liver	Liver

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