Variant report

Variant	rs942317
Chromosome Location	chr14:56023822-56023823
allele	A/C
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	ESR1	chr14:56023333-56024471	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr14:56023419-56024619	ECC-1	luminal epithelium:	n/a	chr14:56024071-56024088
3	FOXM1	chr14:56023500-56024575	ECC-1	luminal epithelium:	n/a	n/a
4	SIN3AK20	chr14:56023636-56024499	MCF-7	breast:	n/a	n/a
5	TCF12	chr14:56023607-56024632	ECC-1	luminal epithelium:	n/a	chr14:56024058-56024066 chr14:56024390-56024397
6	TEAD4	chr14:56023819-56024455	MCF-7	breast:	n/a	n/a
7	GATA3	chr14:56023771-56024115	SH-SY5Y	brain:	n/a	chr14:56023872-56023881
8	EP300	chr14:56023468-56024565	ECC-1	luminal epithelium:	n/a	n/a
9	REST	chr14:56023314-56024419	ECC-1	luminal epithelium:	n/a	chr14:56024025-56024045 chr14:56024031-56024045 chr14:56024030-56024039
10	JUND	chr14:56023790-56024555	SK-N-SH	brain:	n/a	chr14:56023872-56023883
11	TEAD4	chr14:56023760-56024420	A549	lung:	n/a	n/a
12	NFIC	chr14:56023556-56024536	SK-N-SH	brain:	n/a	chr14:56024071-56024088
13	PBX3	chr14:56023762-56024522	SK-N-SH	brain:	n/a	n/a
14	RAD21	chr14:56023680-56024486	ECC-1	luminal epithelium:	n/a	n/a
15	REST	chr14:56023781-56024313	A549	lung:	n/a	chr14:56024025-56024045 chr14:56024031-56024045 chr14:56024030-56024039
16	EP300	chr14:56023756-56024535	ECC-1	luminal epithelium:	n/a	n/a
17	GATA3	chr14:56023753-56024315	T-47D	breast:	n/a	chr14:56023872-56023881
18	GATA3	chr14:56023667-56024528	SK-N-SH	brain:	n/a	chr14:56023872-56023881
19	TEAD4	chr14:56023573-56024521	ECC-1	luminal epithelium:	n/a	n/a
20	REST	chr14:56023705-56024418	MCF-7	breast:	n/a	chr14:56024025-56024045 chr14:56024031-56024045 chr14:56024030-56024039
21	REST	chr14:56023745-56024380	ECC-1	luminal epithelium:	n/a	chr14:56024025-56024045 chr14:56024031-56024045 chr14:56024030-56024039
22	TEAD4	chr14:56023541-56024490	ECC-1	luminal epithelium:	n/a	n/a
23	MAX	chr14:56023819-56024501	MCF-7	breast:	n/a	n/a
24	NFIC	chr14:56023452-56024530	ECC-1	luminal epithelium:	n/a	chr14:56024071-56024088
25	EP300	chr14:56023723-56024610	SK-N-SH	brain:	n/a	n/a
26	MXI1	chr14:56023631-56024621	SK-N-SH	brain:	n/a	n/a
27	GATA3	chr14:56023751-56024359	T-47D	breast:	n/a	chr14:56023872-56023881
28	ESR1	chr14:56023465-56024443	ECC-1	luminal epithelium:	n/a	n/a
29	EP300	chr14:56023749-56024363	T-47D	breast:	n/a	n/a
30	TCF12	chr14:56023611-56024581	SK-N-SH	brain:	n/a	chr14:56024058-56024066 chr14:56024390-56024397
31	HDAC2	chr14:56023735-56024565	MCF-7	breast:	n/a	n/a
32	CEBPB	chr14:56023669-56024573	ECC-1	luminal epithelium:	n/a	n/a
33	GATA3	chr14:56023526-56024511	MCF-7	breast:	n/a	chr14:56023872-56023881
34	POLR2A	chr14:56023802-56024414	SK-N-SH	brain:	n/a	n/a
35	NFIC	chr14:56023753-56024480	SK-N-SH	brain:	n/a	chr14:56024071-56024088
36	USF1	chr14:56023821-56024349	SK-N-SH	brain:	n/a	chr14:56024120-56024141
37	FOSL2	chr14:56023748-56024544	SK-N-SH	brain:	n/a	chr14:56023872-56023883
38	REST	chr14:56023562-56024409	MCF-7	breast:	n/a	chr14:56024025-56024045 chr14:56024031-56024045 chr14:56024030-56024039
39	ZBTB33	chr14:56023768-56024413	SK-N-SH	brain:	n/a	n/a
40	JUND	chr14:56023749-56024516	SK-N-SH	brain:	n/a	chr14:56023872-56023883
41	EP300	chr14:56023381-56024597	SK-N-SH	brain:	n/a	n/a
42	RCOR1	chr14:56023395-56024439	IMR90	lung:	n/a	n/a
43	TCF12	chr14:56023598-56024543	SK-N-SH	brain:	n/a	chr14:56024058-56024066 chr14:56024390-56024397
44	GATA3	chr14:56023597-56024619	SK-N-SH	brain:	n/a	chr14:56023872-56023881
45	SP1	chr14:56023813-56024402	A549	lung:	n/a	n/a
46	TCF12	chr14:56023618-56024503	ECC-1	luminal epithelium:	n/a	chr14:56024058-56024066 chr14:56024390-56024397
47	CEBPB	chr14:56023775-56024472	MCF-7	breast:	n/a	n/a
48	REST	chr14:56023779-56024375	SK-N-SH	brain:	n/a	chr14:56024025-56024045 chr14:56024031-56024045 chr14:56024030-56024039
49	GATA3	chr14:56023717-56024508	MCF-7	breast:	n/a	chr14:56023872-56023881
50	FOS	chr14:56023727-56024323	MCF10A-Er-Src	breast:	n/a	chr14:56023872-56023883

No.	Distal block	Cell Line	Cell type
1	chr14:56008500..56010380-chr14:56023755..56025494,2	MCF-7	breast:
2	chr14:56022620..56026445-chr14:56044953..56047966,3	MCF-7	breast:
3	chr14:56012207..56014964-chr14:56021875..56024671,2	MCF-7	breast:

Variant related genes	Relation type
KTN1	TF binding region
ENSG00000213641	Chromatin interaction
ENSG00000271484	Chromatin interaction
ENSG00000126777	Chromatin interaction
ENSG00000186615	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10136386	0.84[CEU][hapmap]
rs10145555	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444721	0.81[CEU][hapmap]
rs12587735	0.81[CEU][hapmap]
rs12882850	0.81[CEU][hapmap]
rs12897227	0.81[CEU][hapmap]
rs1951887	0.81[CEU][hapmap]
rs2296182	0.84[CEU][hapmap]
rs28393008	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28599919	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3736877	0.81[JPT][hapmap]
rs3765515	0.80[CEU][hapmap]
rs3783654	0.81[JPT][hapmap]
rs4457912	0.81[CEU][hapmap]
rs4901585	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4901587	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4901588	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4901589	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs61976601	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6573038	0.82[JPT][hapmap];0.91[MEX][hapmap]
rs6573054	0.81[CEU][hapmap]
rs755073	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8007832	0.81[CEU][hapmap]
rs8011732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1047054	chr14:55922287-56035579	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1037161	chr14:55928030-56039353	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs942317	WDHD1	cis	cerebellum	SCAN
rs942317	GCH1	cis	cerebellum	SCAN
rs942317	CNIH	cis	cerebellum	SCAN
rs942317	KTN1	cis	parietal	SCAN
rs942317	KTN1	cis	cerebellum	SCAN
rs942317	PTGDR	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56010600-56026600	Weak transcription	Right Ventricle	heart
2	chr14:56010800-56024000	Weak transcription	A549	lung
3	chr14:56014000-56024000	Weak transcription	Pancreas	Pancrea
4	chr14:56014000-56031200	Weak transcription	Left Ventricle	heart
5	chr14:56020800-56024000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr14:56021000-56024000	Weak transcription	Aorta	Aorta
7	chr14:56021000-56026600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr14:56022200-56024000	Weak transcription	Psoas Muscle	Psoas
9	chr14:56022600-56026600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr14:56023000-56024000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr14:56023200-56024400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr14:56023200-56025000	Enhancers	Fetal Muscle Leg	muscle
13	chr14:56023400-56024000	Enhancers	HSMM	muscle
14	chr14:56023400-56024400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:56023400-56024400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:56023400-56024400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr14:56023400-56024400	Enhancers	Fetal Kidney	kidney
18	chr14:56023400-56024400	Enhancers	Ovary	ovary
19	chr14:56023400-56024400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr14:56023400-56024600	Enhancers	HMEC	breast
21	chr14:56023400-56025200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr14:56023600-56024000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr14:56023600-56024000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr14:56023600-56024000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:56023600-56024000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:56023600-56024000	Flanking Active TSS	Fetal Heart	heart
27	chr14:56023600-56024000	Enhancers	Stomach Smooth Muscle	stomach
28	chr14:56023600-56024400	Enhancers	Colon Smooth Muscle	Colon
29	chr14:56023600-56024400	Enhancers	Fetal Stomach	stomach
30	chr14:56023600-56024400	Enhancers	Osteobl	bone
31	chr14:56023600-56024600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr14:56023600-56024600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr14:56023600-56025000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr14:56023600-56025200	Enhancers	NHDF-Ad	bronchial
35	chr14:56023600-56045200	Weak transcription	Primary T cells from cord blood	blood
36	chr14:56023800-56024000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr14:56023800-56024000	Enhancers	NH-A	brain
38	chr14:56023800-56024200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr14:56023800-56024200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr14:56023800-56024200	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr14:56023800-56024200	Enhancers	Brain Hippocampus Middle	brain
42	chr14:56023800-56024400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr14:56023800-56024400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr14:56023800-56024400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr14:56023800-56024400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr14:56023800-56024400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr14:56023800-56024400	Enhancers	Liver	Liver
48	chr14:56023800-56024400	Enhancers	Fetal Brain Female	brain
49	chr14:56023800-56024400	Enhancers	HSMMtube	muscle
50	chr14:56023800-56024400	Enhancers	NHLF	lung

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