Variant report

Variant	rs531750
Chromosome Location	chr6:25882642-25882643
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:75)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:75 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr6:25882323-25882656	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr6:25882580-25882730	GM12878	blood:	n/a	n/a
3	CTCF	chr6:25882277-25882822	GM12878	blood:	n/a	n/a
4	RAD21	chr6:25882272-25882788	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr6:25882574-25882755	HepG2	liver:	n/a	n/a
6	CTCF	chr6:25882590-25882685	Pancreas_OC	pancreas:	n/a	n/a
7	CTCF	chr6:25882580-25882730	GM12864	blood:	n/a	n/a
8	CTCF	chr6:25882620-25882770	HEK293	kidney:	n/a	n/a
9	CTCF	chr6:25882552-25882727	GM12892	blood:	n/a	n/a
10	CTCF	chr6:25882529-25882719	GM19240	blood:	n/a	n/a
11	CTCF	chr6:25882219-25882780	K562	blood:	n/a	n/a
12	JUND	chr6:25882614-25882790	K562	blood:	n/a	n/a
13	MAX	chr6:25882156-25882831	A549	lung:	n/a	n/a
14	CREB1	chr6:25882215-25882714	H1-hESC	embryonic stem cell:	n/a	n/a
15	TBP	chr6:25882281-25882756	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr6:25882487-25882812	A549	lung:	n/a	n/a
17	CTCF	chr6:25882552-25882724	GM13976	blood:	n/a	n/a
18	CTCF	chr6:25882520-25882670	HRPEpiC	eye:	n/a	n/a
19	CTCF	chr6:25882375-25882829	K562	blood:	n/a	n/a
20	CTCF	chr6:25882564-25882752	GM12878	blood:	n/a	n/a
21	CTCF	chr6:25882558-25882732	GM19239	blood:	n/a	n/a
22	CTCF	chr6:25882620-25882770	GM12866	blood:	n/a	n/a
23	CTCF	chr6:25882582-25882684	GM10266	blood:	n/a	n/a
24	CTCF	chr6:25882540-25882690	K562	blood:	n/a	n/a
25	CTCF	chr6:25882580-25882730	GM12867	blood:	n/a	n/a
26	CTCF	chr6:25882520-25882670	HFF-Myc	foreskin:	n/a	n/a
27	CTCF	chr6:25882063-25883032	A549	lung:	n/a	n/a
28	CTCF	chr6:25882266-25882739	K562	blood:	n/a	n/a
29	ATF2	chr6:25882417-25882763	H1-hESC	embryonic stem cell:	n/a	n/a
30	RAD21	chr6:25882542-25882745	HepG2	liver:	n/a	n/a
31	CTCF	chr6:25882224-25882757	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr6:25882520-25882670	GM12871	blood:	n/a	n/a
33	CTCF	chr6:25882600-25882750	BE2_C	brain:	n/a	n/a
34	CTCF	chr6:25882550-25882735	Lung_OC	lung:	n/a	n/a
35	CTCF	chr6:25882560-25882710	HUVEC	blood vessel:	n/a	n/a
36	CTCF	chr6:25882262-25882738	Spleen_OC	spleen:	n/a	n/a
37	CTCF	chr6:25882503-25882769	A549	lung:	n/a	n/a
38	CTCF	chr6:25882580-25882730	HEK293	kidney:	n/a	n/a
39	CTCF	chr6:25882639-25882731	HUVEC	blood vessel:	n/a	n/a
40	EP300	chr6:25882635-25882811	K562	blood:	n/a	chr6:25882758-25882772
41	CTCF	chr6:25882300-25882712	GM12891	blood:	n/a	n/a
42	RAD21	chr6:25882544-25882769	A549	lung:	n/a	n/a
43	CTCF	chr6:25882554-25882757	K562	blood:	n/a	n/a
44	CTCF	chr6:25882575-25882735	NHEK	skin:	n/a	n/a
45	CTCF	chr6:25882540-25882690	GM12864	blood:	n/a	n/a
46	CTCF	chr6:25882600-25882750	GM12869	blood:	n/a	n/a
47	MYC	chr6:25882545-25882863	K562	blood:	n/a	n/a
48	CTCF	chr6:25882620-25882684	HepG2	liver:	n/a	n/a
49	CTCF	chr6:25882530-25882742	GM19238	blood:	n/a	n/a
50	TAF7	chr6:25882328-25882725	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
SLC17A3	TF binding region
HIST1H2APS2	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs115810	0.88[CHB][hapmap]
rs1165170	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165172	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165201	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs129129	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1540275	0.86[CHB][hapmap]
rs1540276	0.88[CHB][hapmap]
rs169219	1.00[CHB][hapmap]
rs199737	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs199739	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs199741	0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs199743	0.82[ASN][1000 genomes]
rs199748	0.85[ASN][1000 genomes]
rs199751	0.88[CHB][hapmap]
rs199753	0.88[CHB][hapmap]
rs199754	0.86[CHB][hapmap]
rs2230655	0.86[CHB][hapmap]
rs3903852	0.86[JPT][hapmap]
rs428469	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs442601	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs473913	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478349	0.89[ASN][1000 genomes]
rs483906	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517842	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518700	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537581	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629835	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs645279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901039	0.86[CHB][hapmap]
rs6922788	0.86[CHB][hapmap]
rs765285	1.00[YRI][hapmap]
rs7767546	0.84[ASN][1000 genomes]
rs793144	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs807212	0.88[CHB][hapmap]
rs807214	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
5	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
6	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25877000-25883800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:25881600-25884200	Weak transcription	HepG2	liver
3	chr6:25882000-25882800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:25882000-25882800	Active TSS	Primary B cells from peripheral blood	blood
5	chr6:25882000-25882800	Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr6:25882000-25882800	Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr6:25882000-25882800	Active TSS	Osteobl	bone
8	chr6:25882000-25883000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:25882000-25883000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:25882200-25882800	Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:25882200-25882800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr6:25882200-25882800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:25882200-25882800	Enhancers	Fetal Heart	heart
14	chr6:25882200-25882800	ZNF genes & repeats	Fetal Intestine Large	intestine
15	chr6:25882200-25882800	Active TSS	GM12878-XiMat	blood
16	chr6:25882400-25882800	Active TSS	Primary B cells from cord blood	blood
17	chr6:25882400-25882800	Active TSS	Primary T cells fromperipheralblood	blood
18	chr6:25882400-25882800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:25882400-25884400	Weak transcription	Pancreas	Pancrea
20	chr6:25882600-25882800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:25882600-25882800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:25882600-25882800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:25882600-25882800	Active TSS	Adipose Nuclei	Adipose
24	chr6:25882600-25882800	Enhancers	Fetal Muscle Trunk	muscle
25	chr6:25882600-25882800	Enhancers	Placenta	Placenta
26	chr6:25882600-25882800	Enhancers	Fetal Thymus	thymus
27	chr6:25882600-25882800	Enhancers	NHDF-Ad	bronchial
28	chr6:25882600-25883000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:25882600-25883000	Active TSS	Monocytes-CD14+_RO01746	blood
30	chr6:25882600-25883800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:25882600-25883800	Weak transcription	Liver	Liver
32	chr6:25882600-25883800	Weak transcription	HMEC	breast
33	chr6:25882600-25884400	Weak transcription	A549	lung

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