Variant report

Variant	rs538706
Chromosome Location	chr6:149640674-149640675
allele	A/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	chr6:149640157-149641086	MCF10A-Er-Src	breast:	n/a	chr6:149641021-149641031 chr6:149641021-149641031 chr6:149641021-149641031 chr6:149641021-149641030 chr6:149641021-149641031
2	EP300	chr6:149640497-149640928	GM12878	blood:	n/a	chr6:149640718-149640727 chr6:149640894-149640908
3	POLR2A	chr6:149639551-149640750	GM12891	blood:	n/a	n/a
4	CUX1	chr6:149639997-149640975	GM12878	blood:	n/a	chr6:149640315-149640329
5	RUNX3	chr6:149640533-149641043	GM12878	blood:	n/a	n/a
6	NFATC1	chr6:149639550-149641270	GM12878	blood:	n/a	n/a
7	EP300	chr6:149640037-149640868	GM12878	blood:	n/a	chr6:149640718-149640727 chr6:149640277-149640286 chr6:149640392-149640406
8	POLR2A	chr6:149639531-149640800	GM12878	blood:	n/a	n/a
9	FOS	chr6:149640280-149640955	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr6:149640591-149640895	MCF10A-Er-Src	breast:	n/a	n/a
11	ATF2	chr6:149639222-149640982	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:149640436-149640786	GM12892	blood:	n/a	n/a
13	POLR2A	chr6:149637775-149640831	GM12892	blood:	n/a	n/a
14	NFIC	chr6:149639135-149641240	GM12878	blood:	n/a	n/a
15	STAT5A	chr6:149640479-149640833	GM12878	blood:	n/a	n/a
16	RELA	chr6:149639613-149641120	GM12878	blood:	n/a	n/a
17	FOXM1	chr6:149639523-149640979	GM12878	blood:	n/a	n/a
18	STAT3	chr6:149640593-149641151	MCF10A-Er-Src	breast:	n/a	chr6:149641021-149641030
19	ATF2	chr6:149640165-149641065	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:149640621-149640972	MCF10A-Er-Src	breast:	n/a	n/a
21	MYC	chr6:149640060-149640993	MCF10A-Er-Src	breast:	n/a	n/a
22	NFATC1	chr6:149640291-149641234	GM12878	blood:	n/a	n/a
23	STAT3	chr6:149640130-149640861	MCF10A-Er-Src	breast:	n/a	chr6:149640381-149640392 chr6:149640279-149640287
24	E2F4	chr6:149640282-149640685	MCF10A-Er-Src	breast:	n/a	n/a
25	EP300	chr6:149639723-149640944	GM12878	blood:	n/a	chr6:149640718-149640727 chr6:149640277-149640286 chr6:149640392-149640406 chr6:149640894-149640908
26	POLR2A	chr6:149637807-149641059	GM12878	blood:	n/a	n/a
27	MTA3	chr6:149639052-149640814	GM12878	blood:	n/a	n/a
28	TBP	chr6:149639694-149641046	GM12878	blood:	n/a	n/a
29	MEF2A	chr6:149640441-149640989	GM12878	blood:	n/a	chr6:149640443-149640458
30	FOS	chr6:149640621-149640917	MCF10A-Er-Src	breast:	n/a	n/a
31	STAT3	chr6:149640575-149640911	MCF10A-Er-Src	breast:	n/a	n/a
32	STAT3	chr6:149640273-149640984	MCF10A-Er-Src	breast:	n/a	chr6:149640381-149640392 chr6:149640279-149640287

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149538892..149540721-chr6:149638148..149641111,2	MCF-7	breast:
2	chr6:149351823..149355344-chr6:149638842..149641991,4	MCF-7	breast:

Variant related genes	Relation type
TAB2	TF binding region
ENSG00000236591	Chromatin interaction
ENSG00000055208	Chromatin interaction
ENSG00000228408	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs112225	0.83[JPT][hapmap]
rs12110948	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs173140	0.83[EUR][1000 genomes]
rs2031450	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236997	0.89[EUR][1000 genomes]
rs236998	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs236999	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs237000	0.89[EUR][1000 genomes]
rs237004	0.91[JPT][hapmap]
rs237006	0.83[EUR][1000 genomes]
rs237008	0.82[EUR][1000 genomes]
rs237013	0.89[EUR][1000 genomes]
rs237014	0.89[EUR][1000 genomes]
rs237015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs237017	0.89[EUR][1000 genomes]
rs237020	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs237022	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs237027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237030	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237031	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237036	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237037	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs365469	0.94[EUR][1000 genomes]
rs376269	0.83[JPT][hapmap]
rs376757	0.83[JPT][hapmap]
rs377454	0.84[JPT][hapmap]
rs378991	0.83[JPT][hapmap]
rs382720	0.83[JPT][hapmap]
rs388335	0.84[JPT][hapmap]
rs389996	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs394375	0.84[JPT][hapmap]
rs395037	0.83[JPT][hapmap]
rs408451	0.83[JPT][hapmap]
rs409196	0.82[JPT][hapmap]
rs425278	1.00[JPT][hapmap]
rs425540	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs431362	0.84[JPT][hapmap]
rs437931	0.83[JPT][hapmap]
rs439495	0.83[JPT][hapmap]
rs452586	0.83[JPT][hapmap]
rs473864	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474587	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs483877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs506779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520551	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520683	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524092	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537843	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543711	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548925	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs551627	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs558044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559848	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs567816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573684	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576022	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs579666	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs602010	0.83[JPT][hapmap]
rs602094	0.88[JPT][hapmap]
rs6916134	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926840	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7752947	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786751	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015360	chr6:149609804-149649982	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers 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 target site	10 gene(s)	inside rSNPs	diseases
4	esv3365966	chr6:149637634-149640707	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149637200-149640800	Active TSS	A549	lung
2	chr6:149637200-149641000	Active TSS	Primary T killer memory cells from peripheral blood	blood
3	chr6:149637400-149640800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:149637400-149640800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:149637400-149640800	Active TSS	Brain Cingulate Gyrus	brain
6	chr6:149637400-149640800	Active TSS	Fetal Stomach	stomach
7	chr6:149637400-149641000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:149637400-149641200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr6:149637400-149641200	Active TSS	Brain Angular Gyrus	brain
10	chr6:149637400-149641200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:149637400-149641200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr6:149637400-149641200	Active TSS	Stomach Smooth Muscle	stomach
13	chr6:149637400-149641200	Active TSS	HSMMtube	muscle
14	chr6:149637400-149641200	Active TSS	NH-A	brain
15	chr6:149637400-149641600	Active TSS	Brain Substantia Nigra	brain
16	chr6:149637400-149642000	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr6:149637400-149642600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:149637600-149640800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:149637600-149640800	Active TSS	Brain Hippocampus Middle	brain
20	chr6:149637600-149640800	Active TSS	Colon Smooth Muscle	Colon
21	chr6:149637600-149640800	Active TSS	Ovary	ovary
22	chr6:149637600-149640800	Active TSS	Rectal Smooth Muscle	rectum
23	chr6:149637600-149640800	Active TSS	HSMM	muscle
24	chr6:149637600-149641000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:149637600-149641000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:149637600-149641000	Active TSS	Placenta	Placenta
27	chr6:149637600-149641200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:149637600-149641200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:149637600-149641200	Active TSS	Aorta	Aorta
30	chr6:149637600-149641200	Active TSS	Fetal Kidney	kidney
31	chr6:149637600-149641200	Active TSS	NHLF	lung
32	chr6:149637600-149641400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:149637600-149641400	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr6:149637600-149642000	Active TSS	GM12878-XiMat	blood
35	chr6:149637800-149640800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:149637800-149640800	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr6:149637800-149640800	Active TSS	Muscle Satellite Cultured Cells	--
38	chr6:149637800-149640800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:149637800-149641000	Active TSS	Fetal Intestine Large	intestine
40	chr6:149637800-149641200	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr6:149637800-149641200	Active TSS	HMEC	breast
42	chr6:149637800-149641400	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr6:149638000-149641000	Active TSS	Primary monocytes fromperipheralblood	blood
44	chr6:149638000-149641000	Active TSS	Fetal Thymus	thymus
45	chr6:149638000-149641200	Active TSS	Primary T cells fromperipheralblood	blood
46	chr6:149639200-149640800	Active TSS	Fetal Brain Male	brain
47	chr6:149639400-149640800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:149639400-149641000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:149639400-149641000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:149639400-149641000	Active TSS	Right Atrium	heart

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