Variant report

Variant	rs1019210
Chromosome Location	chr6:57182297-57182298
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	STAT1	chr6:57182179-57182745	GM12878	blood:	n/a	chr6:57182508-57182522
2	TBP	chr6:57182227-57182650	HepG2	liver:	n/a	n/a
3	STAT3	chr6:57182226-57182511	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr6:57181405-57182752	HepG2	liver:	n/a	n/a
5	TAF1	chr6:57182204-57182620	GM12892	blood:	n/a	n/a
6	POLR2A	chr6:57182049-57182671	HCT-116	colon:	n/a	n/a
7	TAF1	chr6:57182156-57182728	GM12878	blood:	n/a	n/a
8	EP300	chr6:57182222-57182476	GM12878	blood:	n/a	chr6:57182410-57182419 chr6:57182412-57182426 chr6:57182406-57182420
9	SIN3A	chr6:57181317-57182994	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:57182207-57182782	H1-hESC	embryonic stem cell:	n/a	n/a
11	ELK1	chr6:57182024-57182788	Hela-S3	cervix:	n/a	n/a
12	TBP	chr6:57181291-57182845	Hela-S3	cervix:	n/a	n/a
13	TAF1	chr6:57182203-57182687	PFSK-1	brain:	n/a	n/a
14	JUND	chr6:57181302-57182639	K562	blood:	n/a	n/a
15	SIN3AK20	chr6:57181915-57182699	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr6:57181490-57182660	HCT-116	colon:	n/a	n/a
17	ELF1	chr6:57182154-57182691	HepG2	liver:	n/a	chr6:57182410-57182421 chr6:57182414-57182427 chr6:57182415-57182426
18	SIN3AK20	chr6:57182100-57182903	PANC-1	pancreas:	n/a	n/a
19	ELK4	chr6:57182085-57182863	Hela-S3	cervix:	n/a	chr6:57182413-57182424
20	POLR2A	chr6:57182063-57182780	ECC-1	luminal epithelium:	n/a	n/a
21	SIN3AK20	chr6:57182295-57182591	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr6:57181336-57182728	K562	blood:	n/a	n/a
23	EP300	chr6:57182104-57182622	T-47D	breast:	n/a	chr6:57182410-57182419 chr6:57182412-57182426 chr6:57182406-57182420
24	POLR2A	chr6:57181406-57182690	GM12892	blood:	n/a	n/a
25	RELA	chr6:57181295-57183003	GM15510	blood:	n/a	n/a
26	MAFK	chr6:57182136-57182845	K562	blood:	n/a	n/a
27	YY1	chr6:57181890-57182605	ECC-1	luminal epithelium:	n/a	chr6:57182382-57182393
28	YY1	chr6:57182249-57182587	HCT-116	colon:	n/a	chr6:57182382-57182393
29	PAX5	chr6:57181949-57182614	GM12878	blood:	n/a	chr6:57182409-57182418
30	POLR2A	chr6:57182017-57182650	HUVEC	blood vessel:	n/a	n/a
31	MAX	chr6:57181158-57182915	HCT-116	colon:	n/a	n/a
32	CTCF	chr6:57181177-57182675	SK-N-SH	brain:	n/a	n/a
33	E2F6	chr6:57181377-57183006	K562	blood:	n/a	chr6:57182070-57182087 chr6:57182435-57182447
34	STAT5A	chr6:57181969-57182714	GM12878	blood:	n/a	chr6:57182508-57182522
35	E2F4	chr6:57181313-57182968	MCF10A-Er-Src	breast:	n/a	chr6:57182070-57182087 chr6:57182434-57182445 chr6:57182435-57182447
36	GABPA	chr6:57182085-57182911	MCF-7	breast:	n/a	chr6:57182329-57182343
37	MAX	chr6:57182103-57182664	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr6:57182200-57182682	GM12891	blood:	n/a	n/a
39	POLR2A	chr6:57181346-57182977	K562	blood:	n/a	n/a
40	ELF1	chr6:57182149-57182702	GM12878	blood:	n/a	chr6:57182410-57182421 chr6:57182414-57182427 chr6:57182415-57182426
41	ZC3H11A	chr6:57182150-57182535	K562	blood:	n/a	n/a
42	PML	chr6:57182056-57182674	MCF-7	breast:	n/a	n/a
43	POLR2A	chr6:57182134-57182879	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:57182165-57182691	Gliobla	brain:	n/a	n/a
45	SMC3	chr6:57181212-57182655	Hela-S3	cervix:	n/a	n/a
46	NRF1	chr6:57181390-57182647	GM12878	blood:	n/a	chr6:57182329-57182343 chr6:57182329-57182340
47	POLR2A	chr6:57182064-57182749	Hela-S3	cervix:	n/a	n/a
48	MXI1	chr6:57181158-57183337	SK-N-SH	brain:	n/a	n/a
49	FOXA1	chr6:57182279-57182543	T-47D	breast:	n/a	n/a
50	MAX	chr6:57181300-57182671	A549	lung:	n/a	n/a

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	chr17:41465875..41466501-chr6:57182159..57182913,2	NB4	blood:
6	chr6:57182115..57182634-chrX:46696262..46697000,2	NB4	blood:
7	chr6:57036906..57039086-chr6:57181130..57183954,3	K562	blood:
8	chr6:57085596..57088404-chr6:57180850..57182470,2	MCF-7	breast:
9	chr6:56817510..56820425-chr6:57182215..57184592,2	K562	blood:

Variant related genes	Relation type
PRIM2	TF binding region
ENSG00000226803	Chromatin interaction
ENSG00000112210	Chromatin interaction
ENSG00000112208	Chromatin interaction
ENSG00000102218	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000151914	Chromatin interaction
ENSG00000151917	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1013893	0.87[CHB][hapmap]
rs1013894	0.82[CHB][hapmap]
rs1029872	0.95[CHB][hapmap]
rs10733187	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1119375	0.82[CHB][hapmap]
rs12664535	0.82[CHB][hapmap]
rs1618210	0.95[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap]
rs1741916	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1755833	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[MKK][hapmap]
rs2013464	0.81[CHB][hapmap]
rs2013480	0.95[CHB][hapmap]
rs2098172	0.91[CHB][hapmap]
rs2191651	0.82[CHB][hapmap]
rs2215511	0.95[CHB][hapmap]
rs3757294	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3800015	0.87[CHB][hapmap]
rs4288209	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap]
rs4712144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712149	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs4712154	0.82[CHB][hapmap]
rs4715654	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715655	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.88[MKK][hapmap]
rs4715656	0.95[CHB][hapmap]
rs4715657	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap]
rs6459191	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6459193	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap]
rs7738530	0.91[CHB][hapmap]
rs7771738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296865	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9357943	0.95[CHB][hapmap]
rs9357944	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs9396278	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs980327	0.87[CHB][hapmap]

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	chr6:57181400-57182600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:57181400-57182600	Active TSS	Primary B cells from peripheral blood	blood
24	chr6:57181400-57182600	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr6:57181400-57182600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr6:57181400-57182600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:57181400-57182600	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr6:57181400-57182600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr6:57181400-57182600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr6:57181400-57182600	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr6:57181400-57182600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:57181400-57182600	Active TSS	Muscle Satellite Cultured Cells	--
33	chr6:57181400-57182600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:57181400-57182600	Active TSS	Liver	Liver
35	chr6:57181400-57182600	Active TSS	Brain Germinal Matrix	brain
36	chr6:57181400-57182600	Active TSS	Brain Substantia Nigra	brain
37	chr6:57181400-57182600	Active TSS	Duodenum Mucosa	Duodenum
38	chr6:57181400-57182600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr6:57181400-57182600	Active TSS	Fetal Muscle Leg	muscle
40	chr6:57181400-57182600	Active TSS	Fetal Thymus	thymus
41	chr6:57181400-57182600	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr6:57181400-57182600	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr6:57181400-57182600	Active TSS	HSMMtube	muscle
44	chr6:57181400-57182600	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr6:57181400-57182600	Active TSS	NH-A	brain
46	chr6:57181400-57182800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:57181400-57182800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:57181400-57182800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:57181400-57182800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:57181400-57182800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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