Variant report

Variant	rs729437
Chromosome Location	chr14:104093521-104093522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr14:104093230-104093903	MCF-7	breast:	n/a	n/a
2	FOXA1	chr14:104093404-104093852	T-47D	breast:	n/a	n/a
3	GATA3	chr14:104093267-104093909	T-47D	breast:	n/a	chr14:104093617-104093625
4	GATA3	chr14:104093309-104093871	T-47D	breast:	n/a	chr14:104093617-104093625
5	POLR2A	chr14:104093507-104093536	MCF10A-Er-Src	breast:	n/a	n/a
6	JUND	chr14:104093286-104093961	T-47D	breast:	n/a	n/a
7	GATA2	chr14:104093411-104093749	SH-SY5Y	brain:	n/a	n/a
8	GATA3	chr14:104093356-104093909	MCF-7	breast:	n/a	chr14:104093617-104093625
9	POLR2A	chr14:104092636-104093638	HepG2	liver:	n/a	n/a
10	ZNF217	chr14:104093448-104093752	MCF-7	breast:	n/a	n/a
11	MAX	chr14:104093317-104096567	MCF-7	breast:	n/a	n/a
12	GATA3	chr14:104093210-104094971	MCF-7	breast:	n/a	chr14:104094458-104094475 chr14:104093617-104093625
13	TCF7L2	chr14:104093472-104093778	MCF-7	breast:	n/a	n/a
14	SRF	chr14:104093176-104094190	MCF-7	breast:	n/a	n/a
15	HDAC2	chr14:104093267-104096451	MCF-7	breast:	n/a	n/a
16	NR2F2	chr14:104093212-104093937	MCF-7	breast:	n/a	n/a
17	EP300	chr14:104093331-104093822	T-47D	breast:	n/a	n/a
18	IRF1	chr14:104093469-104093636	K562	blood:	n/a	n/a
19	GATA3	chr14:104093411-104093787	MCF-7	breast:	n/a	chr14:104093617-104093625
20	EP300	chr14:104093390-104093868	T-47D	breast:	n/a	n/a
21	FOXA1	chr14:104093329-104093872	T-47D	breast:	n/a	n/a
22	GATA3	chr14:104093119-104094099	MCF-7	breast:	n/a	chr14:104093617-104093625
23	SIN3AK20	chr14:104093260-104094028	MCF-7	breast:	n/a	n/a
24	JUND	chr14:104093325-104093909	T-47D	breast:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:104092649..104097026-chr14:104179930..104185119,7	MCF-7	breast:
2	chr14:104092617..104095465-chr14:104143281..104145342,2	MCF-7	breast:
3	chr14:104026823..104028811-chr14:104092754..104094269,2	K562	blood:
4	chr14:104026845..104031617-chr14:104090112..104098528,12	MCF-7	breast:
5	chr14:104093419..104097122-chr14:104180603..104183015,4	K562	blood:
6	chr14:104091773..104098220-chr14:104179036..104183968,10	MCF-7	breast:
7	chr14:104092924..104095729-chr14:104175116..104177946,2	K562	blood:
8	chr14:103988024..103990288-chr14:104092958..104094825,2	K562	blood:
9	chr14:104093231..104097862-chr14:104156769..104161796,10	MCF-7	breast:
10	chr14:103993804..103996722-chr14:104093257..104094770,2	MCF-7	breast:
11	chr14:104026767..104030601-chr14:104092111..104097061,5	MCF-7	breast:
12	chr14:104038550..104040272-chr14:104093339..104095462,2	MCF-7	breast:
13	chr14:104091792..104094435-chr14:104270981..104273053,2	MCF-7	breast:
14	chr14:104088488..104094508-chr14:104095620..104100899,7	K562	blood:
15	chr14:104092924..104097008-chr14:104171636..104177946,5	K562	blood:

No data

Variant related genes	Relation type
KLC1	TF binding region
ENSG00000256053	Chromatin interaction
ENSG00000269910	Chromatin interaction
ENSG00000224997	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000269940	Chromatin interaction
ENSG00000126214	Chromatin interaction
ENSG00000166170	Chromatin interaction
ENSG00000166166	Chromatin interaction
ENSG00000166165	Chromatin interaction
ENSG00000126215	Chromatin interaction
ENSG00000260285	Chromatin interaction
ENSG00000269963	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10047805	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10131067	0.84[AMR][1000 genomes]
rs1054080	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11160756	0.80[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11625397	0.82[JPT][hapmap];0.91[MEX][hapmap]
rs11626589	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11848721	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11850979	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12879004	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12897511	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2296483	0.82[JPT][hapmap];0.96[MEX][hapmap]
rs2403202	0.91[CEU][hapmap]
rs2403203	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28798508	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28823639	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2896488	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2896489	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34258128	0.84[EUR][1000 genomes]
rs35015260	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742463	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3742465	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759586	0.95[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4318144	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4374097	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4383078	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4444269	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4464019	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4561394	0.83[ASN][1000 genomes]
rs4900583	0.80[ASN][1000 genomes]
rs4900584	0.80[ASN][1000 genomes]
rs4900586	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4900589	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs4906341	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4906342	0.85[EUR][1000 genomes]
rs4906348	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4906349	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4906355	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4906358	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61995761	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7154572	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7155511	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7156832	0.83[ASN][1000 genomes]
rs7157116	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7161125	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs745079	0.81[ASW][hapmap];0.90[CEU][hapmap];0.80[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs752624	0.82[JPT][hapmap];0.91[MEX][hapmap]
rs8003289	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs8005540	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8007489	0.82[ASW][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap]
rs8007903	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs8007915	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8008451	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8018214	0.84[ASN][1000 genomes]
rs8020099	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8021368	0.86[ASW][hapmap];0.82[CEU][hapmap];0.80[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8021904	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs861530	0.86[CEU][hapmap]
rs861537	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes]
rs861544	0.86[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs861545	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs861547	0.80[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8702	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
8	esv3490243	chr14:104083248-104099394	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription 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	28 gene(s)	inside rSNPs	diseases
9	esv3490244	chr14:104083248-104099394	Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
10	nsv902308	chr14:104087209-104211180	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs729437	XRCC3	cis	lymphoblastoid	seeQTL
rs729437	CAMK2G	trans	parietal	SCAN
rs729437	C14orf172	cis	multi-tissue	Pritchard
rs729437	ZFYVE21	cis	Lymphoblastoid	GTEx
rs729437	BRF1	cis	parietal	SCAN
rs729437	BAG5	cis	cerebellum	SCAN
rs729437	ZFYVE21	cis	lymphoblastoid	seeQTL
rs729437	KLC1	cis	parietal	SCAN
rs729437	ZFYVE21	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104089800-104093600	Enhancers	Lung	lung
2	chr14:104090200-104094400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr14:104090200-104094600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr14:104090200-104094600	Enhancers	Placenta	Placenta
5	chr14:104090400-104094200	Weak transcription	Liver	Liver
6	chr14:104090400-104094400	Weak transcription	Aorta	Aorta
7	chr14:104090600-104094000	Weak transcription	Colon Smooth Muscle	Colon
8	chr14:104090800-104094000	Weak transcription	Brain Hippocampus Middle	brain
9	chr14:104090800-104094200	Weak transcription	Fetal Lung	lung
10	chr14:104091000-104094600	Weak transcription	Gastric	stomach
11	chr14:104091400-104094000	Weak transcription	K562	blood
12	chr14:104091400-104094200	Weak transcription	Fetal Heart	heart
13	chr14:104091400-104094400	Weak transcription	Pancreas	Pancrea
14	chr14:104091600-104094000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr14:104091600-104094000	Weak transcription	Right Ventricle	heart
16	chr14:104091600-104094200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr14:104091600-104094200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr14:104091600-104094400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr14:104091600-104094400	Enhancers	Fetal Muscle Trunk	muscle
20	chr14:104091600-104094400	Weak transcription	Psoas Muscle	Psoas
21	chr14:104091800-104094000	Weak transcription	Stomach Mucosa	stomach
22	chr14:104091800-104094200	Weak transcription	Right Atrium	heart
23	chr14:104091800-104094400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr14:104092000-104093800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr14:104092000-104093800	Weak transcription	Colonic Mucosa	Colon
26	chr14:104092000-104094000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:104092000-104094000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr14:104092000-104094000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr14:104092000-104094000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr14:104092000-104094000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:104092000-104094000	Weak transcription	Adipose Nuclei	Adipose
32	chr14:104092000-104094000	Weak transcription	Left Ventricle	heart
33	chr14:104092000-104094000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr14:104092000-104094000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr14:104092000-104094000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr14:104092000-104094000	Weak transcription	Small Intestine	intestine
37	chr14:104092000-104094000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr14:104092000-104094000	Enhancers	Hela-S3	cervix
39	chr14:104092000-104094000	Weak transcription	NH-A	brain
40	chr14:104092000-104094000	Weak transcription	NHLF	lung
41	chr14:104092000-104094200	Weak transcription	Brain Substantia Nigra	brain
42	chr14:104092000-104094200	Weak transcription	HUVEC	blood vessel
43	chr14:104092000-104094200	Weak transcription	Osteobl	bone
44	chr14:104092000-104094400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr14:104092000-104094400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr14:104092000-104094400	Weak transcription	Fetal Stomach	stomach
47	chr14:104092200-104093800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr14:104092200-104094000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr14:104092200-104094000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr14:104092200-104094000	Weak transcription	NHEK	skin

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