Variant report

Variant	rs6773261
Chromosome Location	chr3:48675064-48675065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:48674940-48675090	HEK293	kidney:	n/a	n/a
2	FOXA1	chr3:48674657-48675153	HepG2	liver:	n/a	n/a
3	CTCF	chr3:48674980-48675130	HCPEpiC	choroid plexus:	n/a	n/a
4	CTCF	chr3:48674957-48675078	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr3:48675000-48675150	GM06990	blood:	n/a	n/a
6	FOXA1	chr3:48674784-48675122	HepG2	liver:	n/a	n/a
7	CTCF	chr3:48674980-48675130	GM12873	blood:	n/a	n/a
8	CTCF	chr3:48674960-48675110	AG04449	skin:	n/a	n/a
9	CTCF	chr3:48674920-48675070	HepG2	liver:	n/a	n/a
10	FOXA1	chr3:48674640-48675138	HepG2	liver:	n/a	n/a
11	FOXA1	chr3:48674340-48675131	HepG2	liver:	n/a	n/a
12	CTCF	chr3:48675000-48675150	HBMEC	blood vessel:	n/a	n/a
13	FOXA2	chr3:48674789-48675100	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48673016..48675610-chr3:48677964..48680393,2	K562	blood:
2	chr3:48670750..48673706-chr3:48674188..48676105,2	MCF-7	breast:
3	chr3:48645479..48647283-chr3:48674459..48676978,2	MCF-7	breast:
4	chr3:48673914..48675991-chr3:48685883..48687496,2	K562	blood:
5	chr3:48667529..48675453-chr3:48697968..48703139,10	MCF-7	breast:
6	chr3:48670890..48672785-chr3:48672866..48675614,2	MCF-7	breast:
7	chr3:48609681..48612514-chr3:48673616..48675208,2	K562	blood:

No data

Variant related genes	Relation type
SLC26A6	TF binding region
ENSG00000225697	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10470687	1.00[JPT][hapmap]
rs11557629	0.81[AMR][1000 genomes]
rs11706203	0.81[AMR][1000 genomes]
rs11706983	0.81[AMR][1000 genomes]
rs11719291	0.81[AMR][1000 genomes]
rs12107252	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12107418	0.90[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12715429	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13060933	1.00[JPT][hapmap]
rs13063312	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13070798	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13076269	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13090013	0.81[AMR][1000 genomes]
rs13091944	1.00[JPT][hapmap]
rs13094578	0.82[JPT][hapmap]
rs13096357	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13316551	0.81[AMR][1000 genomes]
rs13319651	1.00[JPT][hapmap]
rs13324119	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13324142	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13434258	0.81[AMR][1000 genomes]
rs17080319	0.81[AMR][1000 genomes]
rs2006871	1.00[JPT][hapmap]
rs2276850	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276852	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286651	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286652	0.90[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2302295	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2310996	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2310997	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28452701	0.88[EUR][1000 genomes]
rs2854394	1.00[JPT][hapmap]
rs28567949	0.81[AMR][1000 genomes]
rs28657585	0.81[AMR][1000 genomes]
rs34096717	0.88[EUR][1000 genomes]
rs34153629	0.81[AMR][1000 genomes]
rs34368826	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34577723	0.83[AMR][1000 genomes]
rs34638686	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35064573	0.81[AMR][1000 genomes]
rs35343040	0.81[ASN][1000 genomes]
rs3733086	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821875	1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821876	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57334642	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6768448	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6781283	1.00[JPT][hapmap]
rs6792156	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6792525	1.00[JPT][hapmap]
rs68042649	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6806059	1.00[JPT][hapmap]
rs73078349	0.81[EUR][1000 genomes]
rs740787	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7620853	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7631574	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809222	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9810549	1.00[JPT][hapmap]
rs9811027	0.81[AMR][1000 genomes]
rs9811318	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9812200	0.90[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9812977	0.80[EUR][1000 genomes]
rs9821797	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9830581	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9836462	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9837687	1.00[JPT][hapmap]
rs9841602	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9843316	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9850102	1.00[JPT][hapmap]
rs9868809	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9869698	1.00[JPT][hapmap]
rs9871180	1.00[JPT][hapmap]
rs9873726	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9878063	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9878950	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv876763	chr3:48669648-48710310	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6773261	SLC26A6	cis	lung	GTEx
rs6773261	WDR6	cis	Esophagus Mucosa	GTEx
rs6773261	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs6773261	SLC26A6	cis	Muscle Skeletal	GTEx
rs6773261	WDR6	cis	lung	GTEx
rs6773261	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48673600-48675200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:48673600-48693400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:48673800-48676400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:48673800-48676800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:48673800-48678000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:48673800-48678400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:48673800-48692800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:48674000-48675400	Enhancers	Fetal Muscle Trunk	muscle
9	chr3:48674000-48676600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:48674000-48676600	Weak transcription	Brain Angular Gyrus	brain
11	chr3:48674000-48676600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:48674000-48676800	Weak transcription	NHEK	skin
13	chr3:48674000-48677200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:48674000-48678600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:48674000-48681400	Weak transcription	Pancreas	Pancrea
16	chr3:48674000-48683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:48674000-48692600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:48674000-48693400	Weak transcription	Fetal Brain Male	brain
19	chr3:48674000-48693600	Weak transcription	Brain Substantia Nigra	brain
20	chr3:48674200-48675200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:48674200-48675200	Enhancers	Fetal Heart	heart
22	chr3:48674200-48675200	Enhancers	Fetal Muscle Leg	muscle
23	chr3:48674200-48676600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:48674200-48676800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:48674200-48676800	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:48674200-48692600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:48674400-48675200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:48674400-48675600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:48674400-48676400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:48674400-48676600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:48674400-48677200	Weak transcription	Fetal Intestine Small	intestine
32	chr3:48674400-48677800	Weak transcription	Dnd41	blood
33	chr3:48674400-48682000	Weak transcription	Right Atrium	heart
34	chr3:48674400-48685800	Weak transcription	Fetal Intestine Large	intestine
35	chr3:48674400-48691000	Weak transcription	Spleen	Spleen
36	chr3:48674400-48692800	Weak transcription	Placenta	Placenta
37	chr3:48674400-48692800	Weak transcription	Right Ventricle	heart
38	chr3:48674400-48693600	Weak transcription	Gastric	stomach
39	chr3:48674600-48675200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr3:48674600-48675200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:48674600-48675400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:48674600-48676400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:48674600-48678600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:48674800-48675600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:48674800-48676600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:48674800-48676600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:48674800-48676600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:48674800-48676800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:48674800-48677000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:48674800-48678400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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