Variant report

Variant	rs277630
Chromosome Location	chr3:100054160-100054161
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	POLR2A	chr3:100053789-100054356	U87	brain:	n/a	n/a
2	EP300	chr3:100053854-100054372	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:100053288-100054571	GM18526	blood:	n/a	n/a
4	POLR2A	chr3:100053973-100054744	K562	blood:	n/a	n/a
5	MYC	chr3:100053221-100054645	A549	lung:	n/a	chr3:100054520-100054529
6	RCOR1	chr3:100053387-100054933	K562	blood:	n/a	n/a
7	POLR2A	chr3:100053250-100054516	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr3:100052685-100054939	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:100053313-100055020	K562	blood:	n/a	n/a
10	MXI1	chr3:100053218-100054515	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:100053059-100054674	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr3:100052857-100054783	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:100053112-100054666	GM12878	blood:	n/a	n/a
14	TCF12	chr3:100053364-100054257	A549	lung:	n/a	n/a
15	MXI1	chr3:100053051-100054207	IMR90	lung:	n/a	n/a
16	MAFF	chr3:100053985-100054630	K562	blood:	n/a	n/a
17	MAX	chr3:100052816-100054186	HepG2	liver:	n/a	n/a
18	RELA	chr3:100053197-100054532	GM15510	blood:	n/a	chr3:100054399-100054408 chr3:100054399-100054408
19	POLR2A	chr3:100053124-100054170	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr3:100053236-100054653	GM12891	blood:	n/a	n/a
21	RFX5	chr3:100054129-100054336	GM12878	blood:	n/a	n/a
22	MYC	chr3:100053366-100054557	MCF10A-Er-Src	breast:	n/a	chr3:100054520-100054529
23	POLR2A	chr3:100053276-100054688	HL-60	blood:	n/a	n/a
24	TBP	chr3:100053209-100054712	K562	blood:	n/a	n/a
25	POLR2A	chr3:100053155-100055087	GM12891	blood:	n/a	n/a
26	MAX	chr3:100053086-100054743	NB4	blood:	n/a	chr3:100054520-100054529
27	MXI1	chr3:100053250-100054177	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:100053228-100054809	GM19193	blood:	n/a	n/a
29	POLR2A	chr3:100053130-100054871	GM12892	blood:	n/a	n/a
30	CHD2	chr3:100053187-100054405	GM12878	blood:	n/a	n/a
31	HEY1	chr3:100053398-100054694	K562	blood:	n/a	n/a
32	POLR2A	chr3:100053275-100054529	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:100054147-100054756	HL-60	blood:	n/a	n/a
34	POLR2A	chr3:100053083-100054826	GM12892	blood:	n/a	n/a
35	POLR2A	chr3:100053262-100054565	GM12892	blood:	n/a	n/a
36	MAZ	chr3:100053176-100054422	GM12878	blood:	n/a	n/a
37	SIN3A	chr3:100052952-100054519	H1-hESC	embryonic stem cell:	n/a	n/a
38	TBL1XR1	chr3:100053305-100054382	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:100053142-100054796	GM12878	blood:	n/a	n/a
40	MXI1	chr3:100053113-100054378	HepG2	liver:	n/a	n/a
41	POLR2A	chr3:100053176-100054783	GM12891	blood:	n/a	n/a
42	MAX	chr3:100053229-100054470	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:100053052-100055002	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:100053320-100054599	K562	blood:	n/a	n/a
45	JUND	chr3:100053384-100054685	K562	blood:	n/a	n/a
46	MAX	chr3:100053109-100054670	A549	lung:	n/a	chr3:100054520-100054529
47	POLR2A	chr3:100053194-100054865	Hela-S3	cervix:	n/a	n/a
48	MAX	chr3:100053314-100054791	K562	blood:	n/a	chr3:100054520-100054529
49	MYC	chr3:100053404-100054894	K562	blood:	n/a	chr3:100054520-100054529
50	MAZ	chr3:100053233-100054696	K562	blood:	n/a	chr3:100054520-100054529

No.	Distal block	Cell Line	Cell type
1	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:
2	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
3	chr3:100052074..100055881-chr3:100116822..100121530,5	MCF-7	breast:

Variant related genes	Relation type
NIT2	TF binding region
ENSG00000154174	Chromatin interaction
ENSG00000206535	Chromatin interaction
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1045206	0.93[YRI][hapmap]
rs10936180	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1123578	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1214375	0.90[YRI][hapmap]
rs1214380	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1214381	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228184	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12495001	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1530283	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs166747	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277620	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277622	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277623	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277626	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277628	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277633	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277634	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277635	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277638	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277642	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277644	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277651	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs372438	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772692	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3806615	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs392066	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs402870	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs413425	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs431069	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs432715	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6780662	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs6791102	0.87[ASN][1000 genomes]
rs6794955	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7616634	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7641630	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100052800-100054200	Active TSS	Fetal Kidney	kidney
2	chr3:100052800-100054600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:100052800-100054600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:100052800-100054800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:100052800-100054800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:100053000-100054200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:100053000-100054200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:100053000-100054200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:100053000-100054200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:100053000-100054200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:100053000-100054200	Active TSS	Brain Anterior Caudate	brain
12	chr3:100053000-100054200	Active TSS	Brain Substantia Nigra	brain
13	chr3:100053000-100054200	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr3:100053000-100054200	Active TSS	Fetal Brain Male	brain
15	chr3:100053000-100054200	Active TSS	Fetal Intestine Small	intestine
16	chr3:100053000-100054200	Active TSS	Left Ventricle	heart
17	chr3:100053000-100054200	Active TSS	Sigmoid Colon	Sigmoid Colon
18	chr3:100053000-100054400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:100053000-100054400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr3:100053000-100054400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:100053000-100054400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:100053000-100054400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:100053000-100054400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:100053000-100054400	Active TSS	Aorta	Aorta
25	chr3:100053000-100054400	Active TSS	Brain Angular Gyrus	brain
26	chr3:100053000-100054400	Active TSS	Colonic Mucosa	Colon
27	chr3:100053000-100054400	Active TSS	Psoas Muscle	Psoas
28	chr3:100053000-100054600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr3:100053000-100054600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr3:100053000-100054600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:100053000-100054600	Active TSS	Rectal Smooth Muscle	rectum
32	chr3:100053000-100054600	Active TSS	HSMM	muscle
33	chr3:100053200-100054200	Active TSS	H1 Cell Line	embryonic stem cell
34	chr3:100053200-100054200	Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr3:100053200-100054200	Active TSS	Brain Cingulate Gyrus	brain
36	chr3:100053200-100054200	Active TSS	Colon Smooth Muscle	Colon
37	chr3:100053200-100054200	Active TSS	Gastric	stomach
38	chr3:100053200-100054200	Active TSS	Lung	lung
39	chr3:100053200-100054200	Active TSS	Placenta Amnion	Placenta Amnion
40	chr3:100053200-100054200	Active TSS	Small Intestine	intestine
41	chr3:100053200-100054400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr3:100053200-100054400	Active TSS	Fetal Brain Female	brain
43	chr3:100053200-100054400	Active TSS	Right Ventricle	heart
44	chr3:100053400-100054200	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr3:100053400-100054200	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr3:100053400-100054200	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr3:100053400-100054200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr3:100053400-100054200	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr3:100053400-100054200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:100053400-100054200	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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