Variant report

Variant	rs1888266
Chromosome Location	chr6:57182068-57182069
allele	G/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	chr6:57181405-57182752	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:57182049-57182671	HCT-116	colon:	n/a	n/a
3	SIN3A	chr6:57181317-57182994	H1-hESC	embryonic stem cell:	n/a	n/a
4	ELK1	chr6:57182024-57182788	Hela-S3	cervix:	n/a	n/a
5	TBP	chr6:57181291-57182845	Hela-S3	cervix:	n/a	n/a
6	JUND	chr6:57181302-57182639	K562	blood:	n/a	n/a
7	SIN3AK20	chr6:57181915-57182699	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr6:57181490-57182660	HCT-116	colon:	n/a	n/a
9	POLR2A	chr6:57182063-57182780	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr6:57181336-57182728	K562	blood:	n/a	n/a
11	POLR2A	chr6:57181406-57182690	GM12892	blood:	n/a	n/a
12	RELA	chr6:57181295-57183003	GM15510	blood:	n/a	n/a
13	YY1	chr6:57181890-57182605	ECC-1	luminal epithelium:	n/a	chr6:57182382-57182393
14	PAX5	chr6:57181949-57182614	GM12878	blood:	n/a	chr6:57182409-57182418
15	POLR2A	chr6:57182017-57182650	HUVEC	blood vessel:	n/a	n/a
16	MAX	chr6:57181158-57182915	HCT-116	colon:	n/a	n/a
17	CTCF	chr6:57181177-57182675	SK-N-SH	brain:	n/a	n/a
18	E2F6	chr6:57181377-57183006	K562	blood:	n/a	chr6:57182070-57182087 chr6:57182435-57182447
19	STAT5A	chr6:57181969-57182714	GM12878	blood:	n/a	chr6:57182508-57182522
20	E2F4	chr6:57181313-57182968	MCF10A-Er-Src	breast:	n/a	chr6:57182070-57182087 chr6:57182434-57182445 chr6:57182435-57182447
21	POLR2A	chr6:57181346-57182977	K562	blood:	n/a	n/a
22	ZNF143	chr6:57181273-57182189	K562	blood:	n/a	n/a
23	PML	chr6:57182056-57182674	MCF-7	breast:	n/a	n/a
24	SMC3	chr6:57181212-57182655	Hela-S3	cervix:	n/a	n/a
25	NRF1	chr6:57181390-57182647	GM12878	blood:	n/a	chr6:57182329-57182343 chr6:57182329-57182340
26	POLR2A	chr6:57182064-57182749	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr6:57181158-57183337	SK-N-SH	brain:	n/a	n/a
28	CTCF	chr6:57182040-57182190	NB4	blood:	n/a	n/a
29	MAX	chr6:57181300-57182671	A549	lung:	n/a	n/a
30	POLR2A	chr6:57181324-57183072	GM12891	blood:	n/a	n/a
31	MXI1	chr6:57181072-57182912	IMR90	lung:	n/a	n/a
32	ELF1	chr6:57182033-57182807	SK-N-SH	brain:	n/a	chr6:57182410-57182421 chr6:57182414-57182427 chr6:57182415-57182426
33	POLR2A	chr6:57182064-57182706	HUVEC	blood vessel:	n/a	n/a
34	ELK1	chr6:57181906-57182644	K562	blood:	n/a	n/a
35	POLR2A	chr6:57182011-57183117	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr6:57181131-57182585	A549	lung:	n/a	n/a
37	PML	chr6:57181238-57182844	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:57181940-57182826	PFSK-1	brain:	n/a	n/a
39	PML	chr6:57181928-57182746	K562	blood:	n/a	n/a
40	MAX	chr6:57181207-57182817	ECC-1	luminal epithelium:	n/a	n/a
41	MAX	chr6:57181272-57182670	K562	blood:	n/a	n/a
42	CTCF	chr6:57182040-57182190	NHLF	lung:	n/a	n/a
43	POLR2A	chr6:57181970-57182910	MCF-7	breast:	n/a	n/a
44	MXI1	chr6:57181299-57182675	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:57181303-57182623	IMR90	lung:	n/a	n/a
46	GABPA	chr6:57182031-57182858	SK-N-SH	brain:	n/a	chr6:57182329-57182343
47	CUX1	chr6:57181289-57182677	K562	blood:	n/a	n/a
48	MXI1	chr6:57181324-57182761	Hela-S3	cervix:	n/a	n/a
49	RUNX3	chr6:57181959-57182731	GM12878	blood:	n/a	n/a
50	YY1	chr6:57182035-57182582	SK-N-SH_RA	brain:	n/a	chr6:57182382-57182393

No.	Distal block	Cell Line	Cell type
1	chr6:56818167..56820292-chr6:57177596..57182762,4	MCF-7	breast:
2	chr11:66741225..66741959-chr6:57181813..57182362,2	Hela-S3	cervix:
3	chr6:56917795..56920630-chr6:57180705..57182325,2	K562	blood:
4	chr6:56818015..56821855-chr6:57180367..57183028,4	K562	blood:
5	chr6:57084710..57087719-chr6:57179458..57182091,4	MCF-7	breast:
6	chr6:57036906..57039086-chr6:57181130..57183954,3	K562	blood:
7	chr6:57085596..57088404-chr6:57180850..57182470,2	MCF-7	breast:

Variant related genes	Relation type
PRIM2	TF binding region
ENSG00000151914	Chromatin interaction
ENSG00000226803	Chromatin interaction
ENSG00000112210	Chromatin interaction
ENSG00000151917	Chromatin interaction
ENSG00000112208	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12180921	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1476852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1741910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1741911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1741912	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1741913	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1741915	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755831	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755832	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1755834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17705499	0.93[ASW][hapmap];0.88[GIH][hapmap];0.92[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap]
rs1860652	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1888265	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28367021	0.86[AFR][1000 genomes]
rs28800513	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3757295	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3778513	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800007	1.00[JPT][hapmap]
rs3800010	1.00[JPT][hapmap]
rs3800014	1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs3800016	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs4615395	0.94[YRI][hapmap]
rs4712146	0.88[YRI][hapmap]
rs4715652	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4992408	0.89[YRI][hapmap]
rs58482037	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58651731	1.00[ASN][1000 genomes]
rs59431929	1.00[ASN][1000 genomes]
rs6459186	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459188	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911273	1.00[ASN][1000 genomes]
rs6911353	0.93[ASW][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6915533	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6916106	0.93[EUR][1000 genomes]
rs6936450	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938582	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7754911	0.86[AFR][1000 genomes]
rs9296875	1.00[JPT][hapmap]
rs9396273	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396274	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9464433	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9464434	1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9464437	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9464438	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9464440	0.93[ASW][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs9475820	1.00[ASN][1000 genomes]
rs9475837	0.87[ASW][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9475840	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9475841	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9475842	0.86[AFR][1000 genomes]
rs9475844	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs9475845	1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9475847	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9475852	1.00[ASN][1000 genomes]
rs9475856	1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs9475861	0.93[ASW][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap]
rs9475862	0.87[ASN][1000 genomes]
rs9475863	1.00[ASN][1000 genomes]
rs9475882	1.00[JPT][hapmap]
rs9475887	1.00[JPT][hapmap];0.87[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	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 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	chr6:57181000-57183200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr6:57181200-57182600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:57181200-57182600	Active TSS	Primary T cells from cord blood	blood
4	chr6:57181200-57182600	Active TSS	Brain Angular Gyrus	brain
5	chr6:57181200-57182600	Active TSS	Brain Anterior Caudate	brain
6	chr6:57181200-57182600	Active TSS	Brain Cingulate Gyrus	brain
7	chr6:57181200-57182600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr6:57181200-57182600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:57181200-57182600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr6:57181200-57182600	Active TSS	Right Atrium	heart
11	chr6:57181200-57182800	Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr6:57181200-57182800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr6:57181200-57183000	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr6:57181200-57183200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr6:57181200-57183200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:57181200-57183200	Active TSS	Fetal Brain Female	brain
17	chr6:57181200-57183200	Active TSS	GM12878-XiMat	blood
18	chr6:57181200-57183400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:57181200-57183400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:57181200-57183600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr6:57181200-57183800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:57181400-57182200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr6:57181400-57182200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr6:57181400-57182600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:57181400-57182600	Active TSS	Primary B cells from peripheral blood	blood
26	chr6:57181400-57182600	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr6:57181400-57182600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr6:57181400-57182600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:57181400-57182600	Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr6:57181400-57182600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr6:57181400-57182600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr6:57181400-57182600	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr6:57181400-57182600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:57181400-57182600	Active TSS	Muscle Satellite Cultured Cells	--
35	chr6:57181400-57182600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:57181400-57182600	Active TSS	Liver	Liver
37	chr6:57181400-57182600	Active TSS	Brain Germinal Matrix	brain
38	chr6:57181400-57182600	Active TSS	Brain Substantia Nigra	brain
39	chr6:57181400-57182600	Active TSS	Duodenum Mucosa	Duodenum
40	chr6:57181400-57182600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr6:57181400-57182600	Active TSS	Fetal Muscle Leg	muscle
42	chr6:57181400-57182600	Active TSS	Fetal Thymus	thymus
43	chr6:57181400-57182600	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr6:57181400-57182600	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr6:57181400-57182600	Active TSS	HSMMtube	muscle
46	chr6:57181400-57182600	Active TSS	Monocytes-CD14+_RO01746	blood
47	chr6:57181400-57182600	Active TSS	NH-A	brain
48	chr6:57181400-57182800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:57181400-57182800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:57181400-57182800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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