Variant report

Variant	rs60559550
Chromosome Location	chr6:31658763-31658764
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	MYC	chr6:31658026-31658833	K562	blood:	n/a	n/a
2	MAFF	chr6:31657859-31658967	K562	blood:	n/a	n/a
3	JUN	chr6:31658016-31658930	K562	blood:	n/a	chr6:31658298-31658308 chr6:31658298-31658308 chr6:31658299-31658307 chr6:31658297-31658309 chr6:31658298-31658308
4	MAFK	chr6:31656979-31659283	K562	blood:	n/a	n/a
5	STAT5A	chr6:31658018-31658945	K562	blood:	n/a	chr6:31658731-31658743 chr6:31658389-31658397 chr6:31658490-31658501
6	POLR2A	chr6:31657863-31658926	K562	blood:	n/a	n/a
7	ZBTB7A	chr6:31658024-31658804	K562	blood:	n/a	chr6:31658590-31658601
8	POLR2A	chr6:31657109-31659087	K562	blood:	n/a	n/a
9	UBTF	chr6:31657987-31658864	K562	blood:	n/a	n/a
10	RCOR1	chr6:31657381-31659089	K562	blood:	n/a	n/a
11	ZC3H11A	chr6:31657497-31658846	K562	blood:	n/a	n/a
12	RCOR1	chr6:31657313-31659070	K562	blood:	n/a	n/a
13	CEBPD	chr6:31657981-31659024	K562	blood:	n/a	n/a
14	ELF1	chr6:31657758-31658997	K562	blood:	n/a	n/a
15	MXI1	chr6:31658022-31658886	K562	blood:	n/a	n/a
16	GTF2F1	chr6:31658135-31658890	K562	blood:	n/a	n/a
17	TEAD4	chr6:31657982-31659061	K562	blood:	n/a	n/a
18	CTCF	chr6:31658254-31658957	K562	blood:	n/a	n/a
19	CHD2	chr6:31658001-31658900	K562	blood:	n/a	n/a
20	HDAC2	chr6:31657830-31658988	K562	blood:	n/a	chr6:31658287-31658296 chr6:31658662-31658676
21	IRF1	chr6:31658036-31658903	K562	blood:	n/a	chr6:31658490-31658502 chr6:31658490-31658502 chr6:31658491-31658501 chr6:31658489-31658503
22	BHLHE40	chr6:31657114-31659036	K562	blood:	n/a	n/a
23	MAZ	chr6:31657943-31658975	K562	blood:	n/a	n/a
24	CEBPB	chr6:31658209-31658902	K562	blood:	n/a	n/a
25	POLR2A	chr6:31657876-31659013	K562	blood:	n/a	n/a
26	ATF3	chr6:31658018-31658902	K562	blood:	n/a	n/a
27	TAL1	chr6:31657996-31658997	K562	blood:	n/a	chr6:31658625-31658634 chr6:31658687-31658695
28	JUN	chr6:31658070-31658885	K562	blood:	n/a	chr6:31658298-31658308 chr6:31658298-31658308 chr6:31658299-31658307 chr6:31658297-31658309 chr6:31658298-31658308
29	ARID3A	chr6:31657959-31659081	K562	blood:	n/a	n/a
30	MAX	chr6:31657291-31659056	K562	blood:	n/a	n/a
31	GATA2	chr6:31658049-31658947	K562	blood:	n/a	chr6:31658688-31658697 chr6:31658286-31658296 chr6:31658288-31658295 chr6:31658286-31658295
32	ELK1	chr6:31658103-31658847	K562	blood:	n/a	n/a
33	GATA1	chr6:31658085-31659041	PBDE	blood:	n/a	chr6:31658688-31658697 chr6:31658286-31658296 chr6:31658288-31658295 chr6:31658286-31658295
34	POLR2A	chr6:31657909-31658808	K562	blood:	n/a	n/a
35	ZMIZ1	chr6:31657803-31658952	K562	blood:	n/a	n/a
36	REST	chr6:31658062-31658793	K562	blood:	n/a	chr6:31658442-31658455
37	MYC	chr6:31657966-31658943	K562	blood:	n/a	n/a
38	STAT5A	chr6:31657830-31659014	K562	blood:	n/a	chr6:31658731-31658743 chr6:31658389-31658397 chr6:31658490-31658501
39	TBP	chr6:31658066-31658789	K562	blood:	n/a	n/a
40	IRF1	chr6:31657934-31659197	K562	blood:	n/a	chr6:31658490-31658502 chr6:31658490-31658502 chr6:31658491-31658501 chr6:31658489-31658503
41	POLR2A	chr6:31658001-31658914	K562	blood:	n/a	n/a
42	GATA1	chr6:31657995-31658915	K562	blood:	n/a	chr6:31658688-31658697 chr6:31658286-31658296 chr6:31658288-31658295 chr6:31658286-31658295
43	IRF1	chr6:31657732-31659320	K562	blood:	n/a	chr6:31658490-31658502 chr6:31658490-31658502 chr6:31658491-31658501 chr6:31658489-31658503
44	PML	chr6:31657684-31659137	K562	blood:	n/a	chr6:31658220-31658228 chr6:31658300-31658309
45	ATF1	chr6:31658033-31658888	K562	blood:	n/a	n/a
46	UBTF	chr6:31658138-31658793	K562	blood:	n/a	n/a
47	TEAD4	chr6:31656869-31659072	K562	blood:	n/a	n/a
48	YY1	chr6:31658613-31659023	K562	blood:	n/a	n/a
49	KAP1	chr6:31658182-31659141	K562	blood:	n/a	chr6:31658220-31658228 chr6:31658300-31658309
50	REST	chr6:31657798-31658866	K562	blood:	n/a	chr6:31658442-31658455 chr6:31658055-31658073

No.	Distal block	Cell Line	Cell type
1	chr6:31656454..31658818-chr6:31801447..31804411,2	MCF-7	breast:
2	chr6:31656167..31662607-chr6:31701760..31709122,7	MCF-7	breast:
3	chr6:31656803..31659218-chr6:31933436..31935775,2	K562	blood:
4	chr6:31657436..31659534-chr6:31697774..31699736,2	MCF-7	breast:
5	chr6:31647696..31650047-chr6:31656817..31658939,2	MCF-7	breast:
6	chr6:31647152..31650140-chr6:31654951..31659176,4	MCF-7	breast:

Variant related genes	Relation type
ABHD16A	TF binding region
ENSG00000201823	Chromatin interaction
ENSG00000213722	Chromatin interaction
ENSG00000204351	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000204428	Chromatin interaction
ENSG00000255152	Chromatin interaction
ENSG00000204410	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11961829	0.91[AFR][1000 genomes]
rs11964779	1.00[EUR][1000 genomes]
rs11965323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966331	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11967206	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2254083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295666	1.00[ASN][1000 genomes]
rs2295667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28399971	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34453162	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713482	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4947252	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4947329	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947330	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59002496	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59114240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60149397	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60900316	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73398259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398298	0.91[AFR][1000 genomes]
rs7382084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9800604	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
15	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31649600-31669400	Weak transcription	HMEC	breast
2	chr6:31650800-31668800	Strong transcription	Thymus	Thymus
3	chr6:31651200-31663400	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:31651200-31668600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:31651600-31660000	Weak transcription	Fetal Kidney	kidney
6	chr6:31651600-31664600	Strong transcription	Fetal Thymus	thymus
7	chr6:31651600-31667800	Strong transcription	Brain Germinal Matrix	brain
8	chr6:31651600-31668600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:31651800-31659800	Weak transcription	Fetal Brain Male	brain
10	chr6:31651800-31665400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:31651800-31669200	Weak transcription	Fetal Heart	heart
12	chr6:31652000-31662200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:31652000-31664600	Strong transcription	Placenta	Placenta
14	chr6:31652000-31665600	Strong transcription	Adipose Nuclei	Adipose
15	chr6:31652000-31668000	Strong transcription	Liver	Liver
16	chr6:31652000-31668600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:31652000-31668600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:31652000-31668600	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:31652000-31668600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr6:31652000-31668800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:31652200-31664800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:31652200-31666000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:31652200-31666000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:31652200-31668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:31652200-31668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:31652200-31668600	Strong transcription	Fetal Stomach	stomach
27	chr6:31652200-31668800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr6:31652400-31665400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:31652400-31668800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:31652600-31666000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:31653400-31667800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:31653600-31661600	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr6:31653600-31663200	Strong transcription	Brain Angular Gyrus	brain
34	chr6:31653600-31663400	Strong transcription	Right Ventricle	heart
35	chr6:31653600-31664800	Strong transcription	Brain Hippocampus Middle	brain
36	chr6:31653600-31665400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:31653600-31665400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:31653600-31665600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:31653600-31665600	Strong transcription	Primary T cells from cord blood	blood
40	chr6:31653600-31667200	Strong transcription	Lung	lung
41	chr6:31653600-31668000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr6:31653600-31668600	Strong transcription	Fetal Muscle Leg	muscle
43	chr6:31653800-31661400	Strong transcription	Pancreas	Pancrea
44	chr6:31653800-31663200	Strong transcription	HSMMtube	muscle
45	chr6:31653800-31663400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:31653800-31665000	Strong transcription	Esophagus	oesophagus
47	chr6:31653800-31665600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:31653800-31665800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr6:31653800-31665800	Strong transcription	Brain Substantia Nigra	brain
50	chr6:31653800-31665800	Strong transcription	Colon Smooth Muscle	Colon

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