Variant report

Variant	rs17060639
Chromosome Location	chr6:100915659-100915660
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr6:100914974-100915963	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr6:100915317-100916351	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:100912882-100916388	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr6:100912776-100916575	H1-neurons	neurons:	n/a	n/a
5	ELF1	chr6:100915280-100915718	GM12878	blood:	n/a	n/a
6	TCF12	chr6:100915475-100915719	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:100915634-100915684	MCF10A-Er-Src	breast:	n/a
2	chr6:100915634-100915684	HIPEpiC	eye:	n/a
3	chr6:100915634-100915684	T-47D	breast:	n/a
4	chr6:100915634-100915684	HCF	heart:	n/a
5	chr6:100915634-100915684	SKMC	muscle:	n/a
6	chr6:100915634-100915684	PANC-1	pancreas:	n/a
7	chr6:100915634-100915684	Jurkat	blood:	n/a
8	chr6:100915634-100915684	SAEC	small airway:	n/a
9	chr6:100915634-100915684	ovcar-3	ovarian:	n/a
10	chr6:100915634-100915684	HL-60	blood:	n/a
11	chr6:100915634-100915684	AG09309	skin:	n/a
12	chr6:100915634-100915684	BJ	skin:	n/a
13	chr6:100915634-100915684	HCPEpiC	choroid plexus:	n/a
14	chr6:100915634-100915684	ProgFib	skin:	n/a
15	chr6:100915634-100915684	Hepatocyte	liver:	n/a
16	chr6:100915634-100915684	SK-N-SH_RA	brain:	n/a
17	chr6:100915634-100915684	Caco-2	colon:	n/a
18	chr6:100915634-100915684	HRPEpiC	eye:	n/a
19	chr6:100915634-100915684	NB4	blood:	n/a
20	chr6:100915634-100915684	H1-hESC	embryonic stem cell:	embryo
21	chr6:100915634-100915684	GM12892	blood:	n/a
22	chr6:100915634-100915684	HUVEC	blood vessel:	n/a
23	chr6:100915634-100915684	NH-A	brain:	n/a
24	chr6:100915634-100915684	A549	lung:	n/a
25	chr6:100915634-100915684	K562	blood:	n/a
26	chr6:100915634-100915684	PrEC	prostate:	n/a
27	chr6:100915634-100915684	AG04450	lung:	fetal
28	chr6:100915634-100915684	IMR90	lung:	fetal
29	chr6:100915634-100915684	HPAEpiC	pulmonary alveolar:	n/a
30	chr6:100915634-100915684	HCM	heart:	n/a
31	chr6:100915634-100915684	SK-N-SH	brain:	n/a
32	chr6:100915634-100915684	U87	brain:	n/a
33	chr6:100915634-100915684	HEEpiC	esophagus:	n/a
34	chr6:100915634-100915684	HRCEpiC	kidney:	n/a
35	chr6:100915634-100915684	MCF-7	breast:	n/a
36	chr6:100915634-100915684	AG04449	skin:	fetal
37	chr6:100915634-100915684	GM19239	blood:	n/a
38	chr6:100915634-100915684	GM06990	blood:	n/a
39	chr6:100915634-100915684	HEK293	kidney:	embryo
40	chr6:100915634-100915684	CMK	blood:	n/a
41	chr6:100915634-100915684	HNPCEpiC	eye:	n/a
42	chr6:100915634-100915684	GM12891	blood:	n/a
43	chr6:100915634-100915684	SK-N-MC	brain:	n/a
44	chr6:100915634-100915684	PFSK-1	brain:	n/a
45	chr6:100915634-100915684	NHBE	bronchial:	n/a
46	chr6:100915634-100915684	AG09319	gingival:	n/a
47	chr6:100915634-100915684	HCT-116	colon:	n/a
48	chr6:100915634-100915684	Hela-S3	cervix:	n/a
49	chr6:100915634-100915684	NT2-D1	testis:	n/a
50	chr6:100915634-100915684	HAEpiC	amniotic membrane:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:100908327..100910621-chr6:100914553..100916127,2	MCF-7	breast:
2	chr6:100887185..100889268-chr6:100914294..100916955,2	MCF-7	breast:

No data

Variant related genes	Relation type
SIM1	TF binding region
SIM1	CpG island

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3798486	0.95[EUR][1000 genomes]
rs3811076	1.00[EUR][1000 genomes]
rs6907169	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6928357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942018	0.82[YRI][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	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100911800-100916000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr6:100912200-100915800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:100913800-100916000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr6:100914400-100915800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr6:100914400-100915800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
6	chr6:100914400-100915800	Bivalent Enhancer	Fetal Thymus	thymus
7	chr6:100914600-100915800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:100914600-100916200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
9	chr6:100914800-100916000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
10	chr6:100915000-100918200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:100915200-100915800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:100915200-100916000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr6:100915200-100916000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
14	chr6:100915400-100915800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
15	chr6:100915400-100915800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:100915600-100915800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:100915600-100915800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:100915600-100915800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:100915600-100915800	Bivalent Enhancer	Adipose Nuclei	Adipose
20	chr6:100915600-100915800	Bivalent Enhancer	Aorta	Aorta
21	chr6:100915600-100915800	Bivalent Enhancer	Brain Germinal Matrix	brain
22	chr6:100915600-100915800	Bivalent Enhancer	Right Atrium	heart
23	chr6:100915600-100915800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
24	chr6:100915600-100916200	Bivalent Enhancer	Liver	Liver
25	chr6:100915600-100917600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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