Variant report

Variant	rs1779267
Chromosome Location	chr1:62177027-62177028
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	FOS	chr1:62176885-62177231	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:62176885-62177227	MCF10A-Er-Src	breast:	n/a	n/a
3	FOSL2	chr1:62176883-62177215	HepG2	liver:	n/a	n/a
4	JUND	chr1:62177000-62177225	K562	blood:	n/a	n/a
5	RFX5	chr1:62176865-62177827	SK-N-SH	brain:	n/a	chr1:62177196-62177211
6	RFX5	chr1:62177025-62177387	K562	blood:	n/a	chr1:62177196-62177211
7	RFX5	chr1:62177007-62177403	HepG2	liver:	n/a	chr1:62177196-62177211
8	ZNF263	chr1:62176990-62177517	HEK293-T-REx	kidney:	n/a	n/a
9	FOXA2	chr1:62176963-62177210	A549	lung:	n/a	n/a
10	RFX5	chr1:62177014-62177387	Hela-S3	cervix:	n/a	chr1:62177196-62177211
11	FOSL2	chr1:62176779-62177246	A549	lung:	n/a	n/a
12	FOSL2	chr1:62176908-62177273	MCF-7	breast:	n/a	n/a
13	FOS	chr1:62176915-62177231	MCF10A-Er-Src	breast:	n/a	n/a
14	JUND	chr1:62176981-62177232	A549	lung:	n/a	n/a
15	JUND	chr1:62177007-62177192	HepG2	liver:	n/a	n/a
16	FOXA2	chr1:62176807-62177173	A549	lung:	n/a	n/a
17	CEBPB	chr1:62176902-62177225	IMR90	lung:	n/a	n/a
18	ZNF384	chr1:62176892-62177212	K562	blood:	n/a	n/a
19	RFX5	chr1:62176787-62177915	IMR90	lung:	n/a	chr1:62177196-62177211

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62173473..62177807-chr1:62188633..62191997,6	K562	blood:

Variant related genes	Relation type
TM2D1	TF binding region
ENSG00000162604	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11207807	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11207808	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11207811	0.87[YRI][hapmap]
rs1151756	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151757	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151759	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151762	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151770	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151771	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151773	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151775	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1151776	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12117475	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12124430	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130241	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12130439	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134102	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12134205	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12134428	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137410	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141280	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12141298	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12143420	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12144284	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286624	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286625	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286626	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286628	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1286629	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1286630	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1286634	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1611797	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1620169	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1692131	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1692132	0.80[EUR][1000 genomes]
rs17378384	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2051135	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051136	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443919	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770089	0.82[AFR][1000 genomes]
rs6662941	0.93[ASN][1000 genomes]
rs6666057	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691402	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6697770	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6698656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs72672375	0.81[EUR][1000 genomes]
rs72672390	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72674608	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536565	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538825	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7539026	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550631	0.90[EUR][1000 genomes];1.00[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	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62138800-62189600	Weak transcription	Psoas Muscle	Psoas
2	chr1:62140000-62189000	Weak transcription	NHLF	lung
3	chr1:62142800-62188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:62146200-62190200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:62158600-62189800	Weak transcription	Pancreas	Pancrea
6	chr1:62161200-62180600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:62161800-62179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:62162600-62177400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:62163400-62181800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:62165000-62189800	Weak transcription	Aorta	Aorta
11	chr1:62165400-62189400	Weak transcription	Fetal Brain Male	brain
12	chr1:62165400-62189600	Weak transcription	Right Ventricle	heart
13	chr1:62165400-62189800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:62166400-62189400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:62166600-62187400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:62166600-62189400	Weak transcription	A549	lung
17	chr1:62166800-62178000	Weak transcription	Brain Angular Gyrus	brain
18	chr1:62166800-62189400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:62167600-62177200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:62168400-62177600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:62169600-62177400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:62169600-62179400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:62169600-62179600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:62169600-62181200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:62170000-62179200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:62171600-62188400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:62172000-62189400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:62172000-62189800	Weak transcription	Gastric	stomach
29	chr1:62173000-62184000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:62173200-62189600	Weak transcription	Colonic Mucosa	Colon
31	chr1:62174000-62189600	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:62174200-62189000	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:62174400-62188800	Weak transcription	Brain Germinal Matrix	brain
34	chr1:62174400-62189800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:62174400-62189800	Weak transcription	Esophagus	oesophagus
36	chr1:62174600-62184800	Weak transcription	HUVEC	blood vessel
37	chr1:62174600-62189200	Weak transcription	HepG2	liver
38	chr1:62174600-62190200	Weak transcription	Small Intestine	intestine
39	chr1:62174800-62177200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:62174800-62178400	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:62174800-62180000	Weak transcription	Fetal Intestine Small	intestine
42	chr1:62174800-62182600	Weak transcription	NHEK	skin
43	chr1:62174800-62189200	Weak transcription	Fetal Brain Female	brain
44	chr1:62174800-62189400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:62174800-62189600	Weak transcription	Primary B cells from cord blood	blood
46	chr1:62174800-62189600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:62174800-62189600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:62174800-62189600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:62174800-62189600	Weak transcription	Left Ventricle	heart
50	chr1:62174800-62189600	Weak transcription	Osteobl	bone

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