Variant report

Variant	rs1275742
Chromosome Location	chr14:70124566-70124567
allele	C/T
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	JUN	chr14:70124340-70125991	K562	blood:	n/a	chr14:70125598-70125608 chr14:70125598-70125608 chr14:70125953-70125965 chr14:70125599-70125608 chr14:70125598-70125608 chr14:70125598-70125608
2	TCF12	chr14:70124533-70125274	ECC-1	luminal epithelium:	n/a	n/a
3	HDAC2	chr14:70124477-70125903	MCF-7	breast:	n/a	chr14:70125274-70125288
4	MAX	chr14:70124554-70125806	ECC-1	luminal epithelium:	n/a	chr14:70124812-70124825 chr14:70124816-70124823 chr14:70125598-70125607
5	MYC	chr14:70124564-70125087	MCF10A-Er-Src	breast:	n/a	chr14:70124812-70124825 chr14:70124816-70124823
6	USF1	chr14:70124560-70125074	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr14:70124429-70125843	MCF-7	breast:	n/a	chr14:70124812-70124825 chr14:70124816-70124823 chr14:70125598-70125607
8	TCF12	chr14:70124392-70125401	ECC-1	luminal epithelium:	n/a	n/a
9	MYC	chr14:70124544-70125066	MCF10A-Er-Src	breast:	n/a	chr14:70124812-70124825 chr14:70124816-70124823
10	NR2F2	chr14:70124470-70125955	MCF-7	breast:	n/a	n/a
11	POLR2A	chr14:70124488-70125153	ECC-1	luminal epithelium:	n/a	n/a
12	EP300	chr14:70124534-70125877	ECC-1	luminal epithelium:	n/a	chr14:70124827-70124841 chr14:70125598-70125607
13	HDAC2	chr14:70124548-70125220	MCF-7	breast:	n/a	n/a
14	MAX	chr14:70124506-70125945	MCF-7	breast:	n/a	chr14:70124812-70124825 chr14:70124816-70124823 chr14:70125598-70125607
15	MAX	chr14:70124512-70125742	ECC-1	luminal epithelium:	n/a	chr14:70124812-70124825 chr14:70124816-70124823 chr14:70125598-70125607

No.	Distal block	Cell Line	Cell type
1	chr14:70121974..70124991-chr14:70161364..70163471,3	K562	blood:
2	chr14:70124205..70126488-chr14:70237428..70239056,2	K562	blood:
3	chr14:70110578..70113027-chr14:70121882..70124631,2	K562	blood:

Variant related genes	Relation type
KIAA0247	TF binding region
ENSG00000100650	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10149246	0.85[CHB][hapmap];0.91[CHD][hapmap]
rs1275745	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1275746	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1275817	0.92[CHB][hapmap];0.94[ASN][1000 genomes]
rs1295826	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.92[ASN][1000 genomes]
rs17107161	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs1743379	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1999722	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2210803	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2332094	0.83[CHB][hapmap]
rs34686932	0.90[ASN][1000 genomes]
rs4899304	0.93[JPT][hapmap]
rs4902745	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60716885	0.92[ASN][1000 genomes]
rs61980729	0.90[ASN][1000 genomes]
rs61980730	0.92[ASN][1000 genomes]
rs6573900	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7143960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7157093	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8006991	0.83[CHB][hapmap]
rs945308	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs945309	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs945310	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs945312	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1049280	chr14:70036804-70172630	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv542124	chr14:70036804-70172630	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1275742	SLC8A3	cis	parietal	SCAN
rs1275742	CCL20	trans	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70104800-70125600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr14:70109800-70125400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr14:70110400-70124600	Weak transcription	Fetal Brain Female	brain
4	chr14:70114000-70125000	Enhancers	Fetal Intestine Large	intestine
5	chr14:70114000-70126400	Enhancers	Left Ventricle	heart
6	chr14:70116000-70125800	Enhancers	Pancreas	Pancrea
7	chr14:70116600-70130400	Weak transcription	Brain Germinal Matrix	brain
8	chr14:70117800-70124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:70117800-70127800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr14:70118000-70124600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr14:70118000-70126600	Weak transcription	Brain Angular Gyrus	brain
12	chr14:70118200-70124600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr14:70118200-70124600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr14:70118400-70124600	Weak transcription	Aorta	Aorta
15	chr14:70118400-70124600	Weak transcription	HSMM	muscle
16	chr14:70118800-70124800	Weak transcription	Fetal Lung	lung
17	chr14:70118800-70124800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr14:70119000-70129200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr14:70119600-70125200	Weak transcription	Primary T cells from cord blood	blood
20	chr14:70120000-70124600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr14:70120000-70124800	Enhancers	Fetal Intestine Small	intestine
22	chr14:70120200-70124600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:70120200-70124600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr14:70120200-70124600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr14:70120200-70125000	Weak transcription	HUVEC	blood vessel
26	chr14:70120200-70126000	Weak transcription	NHLF	lung
27	chr14:70120400-70124600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr14:70120400-70124600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr14:70120800-70129200	Weak transcription	Fetal Kidney	kidney
30	chr14:70121000-70124600	Weak transcription	Brain Anterior Caudate	brain
31	chr14:70121000-70124600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr14:70121000-70124600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr14:70121000-70124600	Weak transcription	Esophagus	oesophagus
34	chr14:70121000-70124600	Weak transcription	Placenta	Placenta
35	chr14:70121000-70125800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr14:70121200-70124600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr14:70121200-70124600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr14:70121200-70124600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr14:70121200-70124600	Weak transcription	Brain Substantia Nigra	brain
40	chr14:70121200-70124600	Weak transcription	Ovary	ovary
41	chr14:70121200-70124600	Weak transcription	Right Ventricle	heart
42	chr14:70121200-70124600	Weak transcription	Spleen	Spleen
43	chr14:70121200-70124800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr14:70121200-70126600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr14:70121400-70124600	Weak transcription	Colonic Mucosa	Colon
46	chr14:70121400-70125000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr14:70121400-70129200	Weak transcription	A549	lung
48	chr14:70122200-70126200	Enhancers	Small Intestine	intestine
49	chr14:70122200-70129600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr14:70122400-70124600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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