Variant report

Variant	rs3753312
Chromosome Location	chr1:169860528-169860529
allele	A/C
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	GATA3	chr1:169859983-169860993	T-47D	breast:	n/a	chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860852-169860862 chr1:169860852-169860861
2	POLR2A	chr1:169860257-169860788	GM12891	blood:	n/a	n/a
3	KAP1	chr1:169859735-169860669	HEK293	kidney:	n/a	n/a
4	ZNF217	chr1:169860419-169860935	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:169860377-169860595	GM12878	blood:	n/a	n/a
6	GATA3	chr1:169860392-169861063	MCF-7	breast:	n/a	chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860852-169860862 chr1:169860852-169860861
7	TCF7L2	chr1:169860494-169860793	MCF-7	breast:	n/a	n/a
8	JUND	chr1:169860297-169860957	T-47D	breast:	n/a	chr1:169860887-169860898
9	POLR2A	chr1:169860176-169860946	GM12891	blood:	n/a	n/a
10	GATA3	chr1:169860320-169861222	MCF-7	breast:	n/a	chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860852-169860862 chr1:169860852-169860861
11	FOXA1	chr1:169860256-169860861	T-47D	breast:	n/a	chr1:169860402-169860414 chr1:169860817-169860829
12	FOXA1	chr1:169860302-169860789	T-47D	breast:	n/a	chr1:169860402-169860414
13	SPI1	chr1:169860179-169860574	GM12891	blood:	n/a	n/a
14	BATF	chr1:169860249-169860769	GM12878	blood:	n/a	n/a
15	TBP	chr1:169860267-169860816	GM12878	blood:	n/a	n/a
16	WRNIP1	chr1:169859975-169860710	GM12878	blood:	n/a	n/a
17	EBF1	chr1:169860194-169861050	GM12878	blood:	n/a	chr1:169860843-169860854
18	HDAC2	chr1:169860368-169860926	MCF-7	breast:	n/a	chr1:169860759-169860773 chr1:169860853-169860862 chr1:169860402-169860411
19	RUNX3	chr1:169860086-169860885	GM12878	blood:	n/a	chr1:169860718-169860733
20	POLR2A	chr1:169860178-169860654	GM12891	blood:	n/a	n/a
21	POLR2A	chr1:169860074-169860811	GM12892	blood:	n/a	n/a
22	POLR2A	chr1:169860289-169860767	GM12891	blood:	n/a	n/a
23	MTA3	chr1:169859892-169861058	GM12878	blood:	n/a	n/a
24	EP300	chr1:169860398-169860965	T-47D	breast:	n/a	chr1:169860401-169860411
25	POLR2A	chr1:169860284-169860726	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:169859946-169860971	GM12891	blood:	n/a	n/a
27	GATA3	chr1:169860406-169861021	T-47D	breast:	n/a	chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860852-169860862 chr1:169860852-169860861
28	NFIC	chr1:169860085-169860828	GM12878	blood:	n/a	n/a
29	SIN3AK20	chr1:169860203-169861057	MCF-7	breast:	n/a	n/a
30	HDAC2	chr1:169860390-169860887	MCF-7	breast:	n/a	chr1:169860759-169860773 chr1:169860853-169860862 chr1:169860402-169860411
31	JUND	chr1:169860351-169861015	MCF-7	breast:	n/a	chr1:169860887-169860898
32	NR2F2	chr1:169860362-169861032	MCF-7	breast:	n/a	n/a
33	MAX	chr1:169860456-169860858	MCF-7	breast:	n/a	n/a
34	RUNX3	chr1:169860107-169860752	GM12878	blood:	n/a	chr1:169860718-169860733
35	SP1	chr1:169860153-169860934	HCT-116	colon:	n/a	n/a
36	MTA3	chr1:169860053-169860783	GM12878	blood:	n/a	n/a
37	MYC	chr1:169860396-169860541	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr1:169860430-169860803	HCT-116	colon:	n/a	n/a
39	POLR2A	chr1:169860190-169860846	GM12878	blood:	n/a	n/a
40	EP300	chr1:169860244-169860913	T-47D	breast:	n/a	chr1:169860401-169860411

No.	Distal block	Cell Line	Cell type
1	chr1:169858457..169860973-chr1:169907396..169909921,2	MCF-7	breast:
2	chr1:169704931..169706505-chr1:169859799..169862220,2	K562	blood:
3	chr1:169763198..169765886-chr1:169860155..169862900,4	K562	blood:
4	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:
5	chr1:169764521..169766056-chr1:169860447..169863119,2	MCF-7	breast:
6	chr1:169770089..169773107-chr1:169860421..169863060,3	K562	blood:
7	chr1:169763198..169765715-chr1:169860443..169862900,3	K562	blood:

Variant related genes	Relation type
SCYL3	TF binding region
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10489175	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10800488	0.90[EUR][1000 genomes]
rs11577641	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11578817	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11579102	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11579254	1.00[CEU][hapmap]
rs11579709	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11581959	0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11582552	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11584208	1.00[CEU][hapmap]
rs11585093	0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11588736	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs11589659	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11589671	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11590604	0.88[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1360294	0.88[CEU][hapmap]
rs1572551	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16828209	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16862683	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[EUR][1000 genomes]
rs16862705	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16862902	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs1928887	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs2420510	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2420511	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34657513	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35196850	0.94[EUR][1000 genomes]
rs3766138	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766139	0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766145	0.89[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766146	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766150	0.89[ASW][hapmap];0.88[CEU][hapmap];0.80[CHB][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3817859	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3917428	0.87[CEU][hapmap]
rs3917432	0.87[CEU][hapmap]
rs41496844	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs4656201	0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656202	1.00[CEU][hapmap]
rs4656718	1.00[ASW][hapmap]
rs4656720	0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4656722	0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4656723	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4656726	0.89[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4656727	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4656732	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs55806711	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57805301	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58111285	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60191157	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60315765	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61806076	0.90[EUR][1000 genomes]
rs61807812	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61807813	0.85[EUR][1000 genomes]
rs61807814	0.83[EUR][1000 genomes]
rs61807817	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61807818	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61807835	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61807840	0.94[EUR][1000 genomes]
rs6685211	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73026253	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169844800-169860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:169845200-169861400	Weak transcription	Right Ventricle	heart
4	chr1:169845200-169861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:169848400-169860600	Weak transcription	Fetal Heart	heart
7	chr1:169851600-169861200	Weak transcription	Aorta	Aorta
8	chr1:169851600-169861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:169852600-169861400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:169852600-169861400	Weak transcription	Brain Germinal Matrix	brain
11	chr1:169852600-169862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:169852800-169861400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:169853800-169861400	Weak transcription	Fetal Stomach	stomach
14	chr1:169855000-169861400	Weak transcription	HSMMtube	muscle
15	chr1:169855200-169861200	Weak transcription	HSMM	muscle
16	chr1:169855400-169861400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:169856000-169861400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:169856000-169861400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:169856200-169861400	Weak transcription	Brain Angular Gyrus	brain
20	chr1:169857400-169861400	Weak transcription	Fetal Brain Female	brain
21	chr1:169857600-169860800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:169857600-169861200	Weak transcription	Hela-S3	cervix
23	chr1:169858000-169860600	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:169858000-169860600	Weak transcription	NHLF	lung
25	chr1:169858000-169860800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:169858000-169860800	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:169858000-169861400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:169858000-169861400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:169858000-169861400	Weak transcription	Fetal Brain Male	brain
30	chr1:169858000-169861400	Weak transcription	K562	blood
31	chr1:169858200-169861200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:169858200-169861200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:169858200-169861400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:169858200-169861400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:169858800-169861200	Enhancers	Liver	Liver
36	chr1:169858800-169861600	Enhancers	Small Intestine	intestine
37	chr1:169859000-169860600	Enhancers	Esophagus	oesophagus
38	chr1:169859000-169861400	Enhancers	Fetal Lung	lung
39	chr1:169859000-169861400	Enhancers	Dnd41	blood
40	chr1:169859000-169861800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:169859000-169861800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr1:169859200-169860600	Enhancers	Right Atrium	heart
43	chr1:169859400-169861400	Weak transcription	Left Ventricle	heart
44	chr1:169859400-169862000	Weak transcription	Ovary	ovary
45	chr1:169859600-169860600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr1:169859600-169860600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:169859600-169861600	Enhancers	Fetal Intestine Small	intestine
48	chr1:169859800-169860600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:169859800-169861400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:169859800-169861400	Enhancers	Duodenum Smooth Muscle	Duodenum

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