Variant report

Variant	rs2227322
Chromosome Location	chr17:38171668-38171669
allele	C/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	NR3C1	chr17:38171591-38172166	A549	lung:	n/a	n/a
2	MYC	chr17:38171313-38171813	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr17:38170522-38172244	HUVEC	blood vessel:	n/a	n/a
4	STAT3	chr17:38170772-38171821	MCF10A-Er-Src	breast:	n/a	chr17:38171013-38171022 chr17:38171014-38171023
5	POLR2A	chr17:38170916-38176213	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr17:38170766-38176716	U87	brain:	n/a	n/a
7	REST	chr17:38171520-38173265	U87	brain:	n/a	chr17:38172955-38172964
8	POLR2A	chr17:38170628-38176722	U87	brain:	n/a	n/a
9	NR3C1	chr17:38171652-38172220	A549	lung:	n/a	n/a
10	POLR2A	chr17:38171303-38175657	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr17:38171620-38171770	Caco-2	colon:	n/a	n/a
12	STAT3	chr17:38170771-38171825	MCF10A-Er-Src	breast:	n/a	chr17:38171013-38171022 chr17:38171014-38171023
13	FOS	chr17:38171367-38171716	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr17:38171205-38176070	U87	brain:	n/a	n/a
15	FOS	chr17:38170778-38171864	MCF10A-Er-Src	breast:	n/a	chr17:38171023-38171032 chr17:38171014-38171022 chr17:38171010-38171021 chr17:38171015-38171022 chr17:38171027-38171036 chr17:38171013-38171023
16	POLR2A	chr17:38170517-38172349	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr17:38170768-38172358	HUVEC	blood vessel:	n/a	n/a
18	FOS	chr17:38170817-38171859	MCF10A-Er-Src	breast:	n/a	chr17:38171014-38171022 chr17:38171013-38171023 chr17:38171027-38171036 chr17:38171023-38171032 chr17:38171015-38171022 chr17:38171010-38171021
19	STAT3	chr17:38170723-38171824	MCF10A-Er-Src	breast:	n/a	chr17:38171013-38171022 chr17:38171014-38171023
20	STAT3	chr17:38170811-38171866	MCF10A-Er-Src	breast:	n/a	chr17:38171013-38171022 chr17:38171014-38171023

No.	Distal block	Cell Line	Cell type
1	chr17:38169401..38172627-chr17:38277979..38280708,3	K562	blood:
2	chr17:38168785..38171760-chr17:38343651..38347238,3	K562	blood:
3	chr17:38170232..38173097-chr17:38181812..38184113,4	MCF-7	breast:
4	chr17:38170609..38173071-chr17:38181273..38184131,2	MCF-7	breast:
5	chr17:38082095..38085117-chr17:38171214..38173786,3	K562	blood:
6	chr17:38082350..38085117-chr17:38171214..38173786,2	K562	blood:

Variant related genes	Relation type
CSF3	TF binding region
ENSG00000265799	TF binding region
ENSG00000238793	Chromatin interaction
ENSG00000264968	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000172057	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000008838	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1042658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078934	0.84[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11655264	0.89[YRI][hapmap]
rs11658328	0.86[YRI][hapmap]
rs11871747	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12600856	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12602172	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12941811	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12950335	0.84[ASN][1000 genomes]
rs2227315	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227336	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241245	0.86[YRI][hapmap]
rs2305482	0.89[YRI][hapmap]
rs3213762	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826331	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3884477	0.86[ASN][1000 genomes]
rs3935280	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3936197	0.86[ASN][1000 genomes]
rs4065321	0.89[YRI][hapmap]
rs4794822	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4794823	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4794824	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795412	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4795414	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4795415	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4795416	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4795418	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4795419	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4795420	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55771023	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55846942	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56922390	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57065891	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57968500	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59925331	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60082402	0.96[EUR][1000 genomes]
rs62065177	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6503530	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6503533	0.83[ASN][1000 genomes]
rs7021	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs709591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208815	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7209755	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221894	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7222039	0.85[ASN][1000 genomes]
rs7502514	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7502912	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7503555	0.84[ASN][1000 genomes]
rs8065443	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs8065519	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8066582	0.89[YRI][hapmap]
rs8066846	0.84[ASN][1000 genomes]
rs8067817	0.85[ASN][1000 genomes]
rs8068260	0.81[ASN][1000 genomes]
rs8070454	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8072548	0.85[ASN][1000 genomes]
rs8073254	0.85[YRI][hapmap]
rs8075668	0.85[YRI][hapmap]
rs8078692	0.84[ASN][1000 genomes]
rs8078723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8081692	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs868150	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9303283	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[ASN][1000 genomes]
rs9303284	0.87[ASN][1000 genomes]
rs9915252	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv908220	chr17:38153473-38175426	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2227322	GSDMA	cis	Artery Aorta	GTEx
rs2227322	PSMD3	cis	Frontal Cortex	GTEx
rs2227322	MED24	cis	Artery Aorta	GTEx
rs2227322	MED24	cis	Nerve Tibial	GTEx
rs2227322	MED24	cis	Thyroid	GTEx
rs2227322	MED24	cis	Artery Tibial	GTEx
rs2227322	GSDMA	cis	lung	GTEx
rs2227322	GSDMA	cis	Esophagus Muscularis	GTEx
rs2227322	GSDMA	cis	Nerve Tibial	GTEx
rs2227322	GSDMA	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38153800-38172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:38154800-38173600	Weak transcription	Thymus	Thymus
3	chr17:38155000-38173600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:38155000-38174000	Weak transcription	Fetal Brain Female	brain
5	chr17:38155800-38171800	Weak transcription	Spleen	Spleen
6	chr17:38166800-38173400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:38166800-38173800	Weak transcription	Primary T cells from cord blood	blood
8	chr17:38166800-38174600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:38167000-38174800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr17:38169200-38172400	Enhancers	NHEK	skin
14	chr17:38169400-38171800	Enhancers	HMEC	breast
15	chr17:38169600-38172400	Enhancers	Stomach Mucosa	stomach
16	chr17:38169600-38172600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:38169600-38173200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:38169600-38175000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr17:38169800-38172200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr17:38169800-38172400	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr17:38169800-38173000	Enhancers	Fetal Stomach	stomach
22	chr17:38169800-38175600	Enhancers	Fetal Lung	lung
23	chr17:38169800-38176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr17:38170000-38171800	Enhancers	HUVEC	blood vessel
25	chr17:38170000-38172000	Enhancers	Lung	lung
26	chr17:38170000-38173200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:38170000-38173600	Enhancers	Fetal Muscle Trunk	muscle
28	chr17:38170000-38174000	Weak transcription	Brain Germinal Matrix	brain
29	chr17:38170000-38174200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:38170000-38174600	Enhancers	Fetal Muscle Leg	muscle
31	chr17:38170000-38175200	Weak transcription	Brain Angular Gyrus	brain
32	chr17:38170000-38175600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:38170000-38176000	Enhancers	Ovary	ovary
34	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr17:38170200-38171800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:38170200-38171800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr17:38170200-38172000	Enhancers	Adipose Nuclei	Adipose
38	chr17:38170200-38172000	Enhancers	Placenta	Placenta
39	chr17:38170200-38172000	Enhancers	Right Atrium	heart
40	chr17:38170200-38172000	Flanking Active TSS	HepG2	liver
41	chr17:38170200-38172200	Enhancers	Duodenum Mucosa	Duodenum
42	chr17:38170200-38172200	Enhancers	Fetal Intestine Small	intestine
43	chr17:38170200-38172400	Enhancers	Fetal Intestine Large	intestine
44	chr17:38170200-38172400	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr17:38170200-38172800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr17:38170200-38173000	Enhancers	Pancreas	Pancrea
47	chr17:38170200-38173800	Weak transcription	Brain Anterior Caudate	brain
48	chr17:38170200-38174400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr17:38170200-38174600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr17:38170200-38175400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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