Variant report

Variant	rs1874228
Chromosome Location	chr17:37775274-37775275
allele	A/G
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	EP300	chr17:37774616-37775314	A549	lung:	n/a	n/a
2	MAX	chr17:37773764-37775308	ECC-1	luminal epithelium:	n/a	chr17:37774569-37774579 chr17:37774548-37774558 chr17:37774166-37774176 chr17:37774889-37774899 chr17:37773959-37773969 chr17:37774398-37774407 chr17:37774297-37774306 chr17:37774115-37774126
3	MAX	chr17:37774626-37775315	ECC-1	luminal epithelium:	n/a	chr17:37774889-37774899
4	MAX	chr17:37773580-37775345	HCT-116	colon:	n/a	chr17:37774569-37774579 chr17:37774548-37774558 chr17:37774166-37774176 chr17:37774889-37774899 chr17:37773959-37773969 chr17:37774398-37774407 chr17:37774297-37774306 chr17:37774115-37774126
5	EBF1	chr17:37775219-37775586	GM12878	blood:	n/a	n/a
6	MAX	chr17:37773369-37775395	A549	lung:	n/a	chr17:37774569-37774579 chr17:37774548-37774558 chr17:37774166-37774176 chr17:37774889-37774899 chr17:37773959-37773969 chr17:37774398-37774407 chr17:37774297-37774306 chr17:37774115-37774126
7	RCOR1	chr17:37775126-37775355	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:37769144..37771005-chr17:37773634..37775729,2	MCF-7	breast:
2	chr17:37774543..37777330-chr17:37885224..37887436,2	K562	blood:
3	chr17:37758356..37760181-chr17:37774194..37775834,2	MCF-7	breast:
4	chr17:37773896..37776239-chr17:37886682..37888820,2	MCF-7	breast:
5	chr17:37773259..37775797-chr17:37912370..37914095,2	MCF-7	breast:
6	chr17:37730305..37732141-chr17:37773715..37775844,2	MCF-7	breast:
7	chr17:37773404..37776321-chr17:37819728..37822241,2	MCF-7	breast:
8	chr17:37773726..37775508-chr17:37899665..37902639,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214546	TF binding region
ENSG00000173991	Chromatin interaction
ENSG00000141741	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1018246	0.86[ASN][1000 genomes]
rs10445306	0.85[CEU][hapmap]
rs1053651	0.94[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10852934	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11651497	0.97[ASN][1000 genomes]
rs11654018	0.85[CEU][hapmap]
rs11658678	0.90[CEU][hapmap]
rs11658786	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11869286	0.88[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12150298	0.80[GIH][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12150603	0.87[ASW][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.86[ASN][1000 genomes]
rs12450559	0.85[CEU][hapmap]
rs12452880	0.85[CEU][hapmap]
rs12453682	0.87[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12940986	0.87[ASW][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs14050	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1476278	0.80[GIH][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1495099	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1495100	0.86[ASN][1000 genomes]
rs1495101	0.86[ASN][1000 genomes]
rs1495102	0.86[ASN][1000 genomes]
rs1565920	0.85[ASN][1000 genomes]
rs1565922	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1877031	0.94[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2247862	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2271308	0.95[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2271309	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2303316	0.85[CEU][hapmap]
rs2313171	0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2517953	0.81[ASN][1000 genomes]
rs2517955	0.87[ASW][hapmap];1.00[YRI][hapmap]
rs2517957	0.89[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs2517958	0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs2934951	0.86[ASN][1000 genomes]
rs2934952	0.86[ASN][1000 genomes]
rs2934953	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2934956	0.86[ASN][1000 genomes]
rs2941503	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2941504	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2941505	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2941506	0.86[ASN][1000 genomes]
rs2952151	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2952152	0.85[ASN][1000 genomes]
rs33953566	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3751903	0.98[ASN][1000 genomes]
rs3764352	0.82[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MKK][hapmap];0.97[ASN][1000 genomes]
rs3764353	0.97[ASN][1000 genomes]
rs3794712	0.94[ASN][1000 genomes]
rs3817160	0.98[ASN][1000 genomes]
rs407307	0.83[ASN][1000 genomes]
rs4239222	0.85[CEU][hapmap]
rs4794814	0.85[CEU][hapmap]
rs4794817	0.98[ASN][1000 genomes]
rs4795388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795389	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795390	0.97[ASN][1000 genomes]
rs7216086	0.85[CEU][hapmap]
rs732083	0.86[ASN][1000 genomes]
rs732084	0.86[ASN][1000 genomes]
rs7501488	0.85[CEU][hapmap]
rs7503069	0.85[CEU][hapmap]
rs7503705	0.85[CEU][hapmap]
rs8065963	0.85[CEU][hapmap]
rs8077172	0.86[ASN][1000 genomes]
rs8078228	0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs879606	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs881844	0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs903501	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs903502	0.81[ASW][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs907087	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs907088	0.86[ASN][1000 genomes]
rs907089	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs907090	0.86[ASN][1000 genomes]
rs907094	0.82[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MKK][hapmap];0.97[ASN][1000 genomes]
rs9303274	0.80[GIH][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs931992	0.94[ASW][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs9675194	0.82[GIH][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs9915323	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9972882	0.84[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
3	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
4	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
5	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	nsv908208	chr17:37749259-37781849	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv908209	chr17:37749259-37790340	Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv908210	chr17:37761202-37781849	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv908211	chr17:37765047-37782410	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv908212	chr17:37765047-37790340	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv457738	chr17:37770005-37831035	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv574991	chr17:37770005-37831035	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	esv3391098	chr17:37773251-37775799	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1874228	PGAP3	cis	Heart Left Ventricle	GTEx
rs1874228	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs1874228	DHRS11	cis	cerebellum	SCAN
rs1874228	SLFN14	cis	parietal	SCAN
rs1874228	CRKRS	Cis_1M	lymphoblastoid	RTeQTL
rs1874228	PGAP3	cis	cerebellum	SCAN
rs1874228	SPACA3	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37771800-37776200	Enhancers	Fetal Brain Male	brain
2	chr17:37773800-37775400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:37773800-37775400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr17:37774600-37775400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr17:37774600-37776000	Flanking Bivalent TSS/Enh	HepG2	liver
6	chr17:37774800-37775400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:37774800-37775400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr17:37774800-37775400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr17:37774800-37775400	Flanking Active TSS	A549	lung
10	chr17:37774800-37775600	Flanking Active TSS	Fetal Brain Female	brain
11	chr17:37775000-37775400	Enhancers	Primary B cells from peripheral blood	blood
12	chr17:37775000-37775400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:37775000-37775400	Enhancers	Brain Cingulate Gyrus	brain
14	chr17:37775000-37775400	Bivalent Enhancer	Fetal Stomach	stomach
15	chr17:37775000-37775400	Enhancers	Right Ventricle	heart
16	chr17:37775000-37775400	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr17:37775000-37775600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:37775000-37775600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr17:37775000-37775600	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr17:37775000-37775600	Flanking Active TSS	Hela-S3	cervix
21	chr17:37775000-37775800	Bivalent Enhancer	Fetal Intestine Large	intestine
22	chr17:37775000-37778400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr17:37775000-37778400	Weak transcription	Brain Substantia Nigra	brain
24	chr17:37775000-37779400	Weak transcription	Left Ventricle	heart
25	chr17:37775000-37782400	Weak transcription	Gastric	stomach
26	chr17:37775200-37775400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr17:37775200-37775400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:37775200-37775400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr17:37775200-37775400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr17:37775200-37775400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:37775200-37775400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr17:37775200-37775400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
33	chr17:37775200-37775400	Enhancers	HMEC	breast
34	chr17:37775200-37775400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
35	chr17:37775200-37775600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
36	chr17:37775200-37775600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr17:37775200-37775600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
38	chr17:37775200-37775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr17:37775200-37775600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:37775200-37775600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr17:37775200-37775600	Enhancers	Colonic Mucosa	Colon
42	chr17:37775200-37775600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr17:37775200-37775600	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr17:37775200-37775600	Bivalent Enhancer	Placenta	Placenta
45	chr17:37775200-37775600	Enhancers	Placenta Amnion	Placenta Amnion
46	chr17:37775200-37775800	Enhancers	Brain Germinal Matrix	brain
47	chr17:37775200-37776000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
48	chr17:37775200-37776000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr17:37775200-37776000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:37775200-37776200	Enhancers	Duodenum Mucosa	Duodenum

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