Variant report

Variant	rs2746071
Chromosome Location	chr1:192777564-192777565
allele	A/G
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	PBX3	chr1:192777533-192778881	SK-N-SH	brain:	n/a	n/a
2	HA-E2F1	chr1:192777358-192778875	MCF-7	breast:	n/a	chr1:192778120-192778129 chr1:192778331-192778343
3	MAX	chr1:192777156-192778721	Hela-S3	cervix:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777173-192777182 chr1:192777174-192777183 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
4	POLR2A	chr1:192777404-192778709	H1-hESC	embryonic stem cell:	n/a	n/a
5	CBX3	chr1:192777423-192778795	K562	blood:	n/a	n/a
6	POLR2A	chr1:192777515-192778670	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:192776886-192778449	HUVEC	blood vessel:	n/a	n/a
8	SMARCB1	chr1:192777183-192778957	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:192777480-192778598	Gliobla	brain:	n/a	n/a
10	POLR2A	chr1:192777445-192778636	A549	lung:	n/a	n/a
11	MAX	chr1:192777466-192778434	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:192777471-192778566	MCF-7	breast:	n/a	n/a
13	MAX	chr1:192777140-192778716	K562	blood:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777173-192777182 chr1:192777174-192777183 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
14	MAX	chr1:192777178-192778641	H1-hESC	embryonic stem cell:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
15	TAF1	chr1:192777406-192778865	H1-neurons	neurons:	n/a	n/a
16	E2F6	chr1:192777536-192778473	K562	blood:	n/a	chr1:192778120-192778129 chr1:192778331-192778343
17	FOSL2	chr1:192777509-192778299	A549	lung:	n/a	n/a
18	KAP1	chr1:192776513-192779169	HEK293	kidney:	n/a	chr1:192777251-192777259 chr1:192776622-192776631
19	MAX	chr1:192777490-192778583	ECC-1	luminal epithelium:	n/a	n/a
20	MAZ	chr1:192777300-192778694	K562	blood:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
21	POLR2A	chr1:192777438-192778558	SK-N-MC	brain:	n/a	n/a
22	NR2F2	chr1:192777013-192778566	K562	blood:	n/a	chr1:192778435-192778450
23	POLR2A	chr1:192777127-192778871	Hela-S3	cervix:	n/a	n/a
24	MYC	chr1:192776444-192778399	MCF10A-Er-Src	breast:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777173-192777182 chr1:192777174-192777183 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
25	WRNIP1	chr1:192777387-192777589	GM12878	blood:	n/a	n/a
26	ZNF143	chr1:192777406-192778462	H1-hESC	embryonic stem cell:	n/a	chr1:192777819-192777837
27	POLR2A	chr1:192777436-192777796	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr1:192777324-192778574	ECC-1	luminal epithelium:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
29	RELA	chr1:192777312-192778424	GM15510	blood:	n/a	n/a
30	POLR2A	chr1:192777524-192778870	GM19193	blood:	n/a	n/a
31	MAX	chr1:192777088-192778407	SK-N-SH	brain:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777173-192777182 chr1:192777174-192777183 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
32	MYC	chr1:192776515-192778884	MCF10A-Er-Src	breast:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777173-192777182 chr1:192777174-192777183 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
33	POLR2A	chr1:192776209-192783463	IMR90	lung:	n/a	n/a
34	TCF7L2	chr1:192777198-192778723	Hela-S3	cervix:	n/a	n/a
35	ELF1	chr1:192777489-192778457	GM12878	blood:	n/a	chr1:192777974-192777986
36	POLR2A	chr1:192777420-192779029	GM12878	blood:	n/a	n/a
37	TAF1	chr1:192777363-192778840	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr1:192776343-192778901	A549	lung:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777173-192777182 chr1:192777174-192777183 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
39	TBP	chr1:192777511-192778805	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr1:192777081-192779607	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr1:192777128-192779184	Hela-S3	cervix:	n/a	n/a
42	E2F6	chr1:192777318-192778580	H1-hESC	embryonic stem cell:	n/a	chr1:192778120-192778129 chr1:192778331-192778343
43	MYC	chr1:192777361-192778329	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr1:192777224-192779265	Hela-S3	cervix:	n/a	n/a
45	BHLHE40	chr1:192777144-192778643	K562	blood:	n/a	chr1:192778021-192778037 chr1:192778035-192778051 chr1:192778033-192778049
46	POLR2A	chr1:192776512-192778631	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr1:192777554-192779796	PBDE	blood:	n/a	n/a
48	SMC3	chr1:192777452-192777626	K562	blood:	n/a	n/a
49	POLR2A	chr1:192777401-192778632	H1-hESC	embryonic stem cell:	n/a	n/a
50	E2F6	chr1:192777427-192778256	A549	lung:	n/a	chr1:192778120-192778129

No.	Distal block	Cell Line	Cell type
1	chr1:192777340..192777996-chr17:20945690..20946550,2	Hela-S3	cervix:
2	chr1:192777388..192778329-chr17:1303225..1303741,2	Hela-S3	cervix:
3	chr1:192776599..192779563-chr1:193090962..193092551,2	K562	blood:
4	chr1:192775702..192778041-chr1:192986871..192988604,2	MCF-7	breast:
5	chr1:192775703..192778053-chr1:193028205..193029898,2	MCF-7	breast:
6	chr1:192773238..192775392-chr1:192775635..192777815,2	K562	blood:
7	chr1:192459062..192461935-chr1:192775675..192778515,2	K562	blood:
8	chr1:192775766..192777613-chr1:192802344..192805276,2	K562	blood:
9	chr1:192777538..192778505-chr7:65540311..65541089,2	Hela-S3	cervix:
10	chr1:192777293..192779700-chr1:193028238..193029983,2	K562	blood:
11	chr1:192777305..192779700-chr1:193027165..193029983,2	K562	blood:

Variant related genes	Relation type
RGS2	TF binding region
ENSG00000116750	Chromatin interaction
ENSG00000221145	Chromatin interaction
ENSG00000126522	Chromatin interaction
ENSG00000108953	Chromatin interaction
ENSG00000124422	Chromatin interaction
ENSG00000134371	Chromatin interaction
ENSG00000116747	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10801151	0.91[CEU][hapmap];0.91[JPT][hapmap];0.99[EUR][1000 genomes]
rs10801152	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10801153	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10801154	0.91[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs10801155	0.84[ASN][1000 genomes]
rs10801156	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10801157	0.85[EUR][1000 genomes]
rs10801158	0.85[EUR][1000 genomes]
rs10921267	0.90[CEU][hapmap];0.97[EUR][1000 genomes]
rs10921268	0.90[EUR][1000 genomes]
rs11586572	0.97[EUR][1000 genomes]
rs12565835	0.97[EUR][1000 genomes]
rs1418718	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16834851	0.95[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs1819741	0.91[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1890398	0.83[ASN][1000 genomes]
rs1890399	0.84[ASN][1000 genomes]
rs1933694	0.86[CHD][hapmap];0.91[JPT][hapmap]
rs2746072	0.93[EUR][1000 genomes]
rs2746073	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs6428136	0.91[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6669632	0.91[EUR][1000 genomes]
rs6684156	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6703040	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs7525778	0.97[EUR][1000 genomes]
rs7534336	0.90[ASN][1000 genomes]
rs7546861	0.97[EUR][1000 genomes]
rs7549721	0.97[EUR][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	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv548660	chr1:192609268-192945348	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192775400-192777600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:192775400-192777800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr1:192775800-192777600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:192775800-192777800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr1:192775800-192778200	Active TSS	Rectal Smooth Muscle	rectum
6	chr1:192776000-192777600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:192776000-192777800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr1:192776000-192777800	Flanking Active TSS	HUVEC	blood vessel
9	chr1:192776000-192778800	Active TSS	Colon Smooth Muscle	Colon
10	chr1:192776200-192777600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:192776200-192777600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr1:192776200-192777600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:192776200-192777600	Flanking Active TSS	Fetal Lung	lung
14	chr1:192776200-192777600	Flanking Active TSS	NHEK	skin
15	chr1:192776200-192777800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr1:192776200-192777800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:192776200-192777800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:192776200-192780600	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr1:192776400-192777600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:192776400-192777600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr1:192776400-192777800	Flanking Active TSS	Osteobl	bone
22	chr1:192776400-192779400	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr1:192776400-192779400	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr1:192776400-192779600	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:192776400-192779800	Active TSS	Ovary	ovary
26	chr1:192776400-192779800	Active TSS	Stomach Mucosa	stomach
27	chr1:192776400-192780600	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr1:192776400-192780600	Active TSS	Aorta	Aorta
29	chr1:192776400-192781200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr1:192776600-192777800	Flanking Active TSS	NH-A	brain
31	chr1:192776600-192779800	Active TSS	Colonic Mucosa	Colon
32	chr1:192776800-192777600	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr1:192776800-192777800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr1:192776800-192779600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:192777000-192777600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:192777000-192777600	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr1:192777000-192777600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr1:192777000-192777600	Flanking Active TSS	A549	lung
39	chr1:192777000-192777600	Flanking Active TSS	HSMMtube	muscle
40	chr1:192777000-192777800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr1:192777000-192780000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:192777000-192781200	ZNF genes & repeats	Fetal Brain Male	brain
43	chr1:192777200-192777600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
44	chr1:192777200-192777600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
45	chr1:192777200-192777600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:192777200-192777600	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr1:192777200-192777600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr1:192777200-192777600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr1:192777200-192777600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:192777200-192777600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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