Variant report

Variant	rs2227333
Chromosome Location	chr17:38174167-38174168
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38173721-38174772	GM12892	blood:	n/a	n/a
2	POLR2A	chr17:38173011-38174885	K562	blood:	n/a	n/a
3	STAT3	chr17:38174032-38174695	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr17:38173369-38174229	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr17:38173672-38174318	SK-N-MC	brain:	n/a	n/a
6	ZNF263	chr17:38173836-38174581	HEK293-T-REx	kidney:	n/a	chr17:38174157-38174178
7	POLR2A	chr17:38170916-38176213	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr17:38173937-38175874	MCF10A-Er-Src	breast:	n/a	chr17:38174947-38174956
9	POLR2A	chr17:38170766-38176716	U87	brain:	n/a	n/a
10	POLR2A	chr17:38170628-38176722	U87	brain:	n/a	n/a
11	POLR2A	chr17:38171303-38175657	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr17:38173854-38176132	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr17:38173296-38175247	K562	blood:	n/a	n/a
14	STAT3	chr17:38174025-38174706	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr17:38174089-38176121	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr17:38173844-38174714	HepG2	liver:	n/a	n/a
17	POLR2A	chr17:38171205-38176070	U87	brain:	n/a	n/a
18	POLR2A	chr17:38173976-38176162	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr17:38173919-38174400	HL-60	blood:	n/a	n/a
20	POLR2A	chr17:38174125-38174783	GM12892	blood:	n/a	n/a
21	POLR2A	chr17:38173172-38174674	Hela-S3	cervix:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38173133..38174723-chr17:38181069..38183425,2	K562	blood:
2	chr17:38171795..38174739-chr17:38253717..38256695,2	K562	blood:
3	chr17:38172520..38175725-chr17:38187607..38191443,4	MCF-7	breast:
4	chr17:38169328..38171805-chr17:38172299..38175519,5	K562	blood:
5	chr17:38172859..38176802-chr17:38178682..38181500,4	K562	blood:
6	chr17:38141745..38144493-chr17:38173834..38176591,2	MCF-7	breast:
7	chr17:38173047..38175621-chr17:38177692..38179979,3	MCF-7	breast:
8	chr17:38171100..38173173-chr17:38173231..38176436,3	K562	blood:
9	chr17:38143597..38146360-chr17:38172431..38175405,3	K562	blood:
10	chr17:38172636..38175341-chr17:38255721..38258482,3	MCF-7	breast:
11	chr17:38172905..38174715-chr17:38255635..38257887,2	MCF-7	breast:
12	chr17:38169328..38171032-chr17:38172943..38175519,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265799	TF binding region
ENSG00000108342	Chromatin interaction
ENSG00000108344	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000126368	Chromatin interaction
ENSG00000265799	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10445310	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11078930	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11078931	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078935	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11078936	0.89[ASN][1000 genomes]
rs11654208	0.89[ASN][1000 genomes]
rs11655264	0.89[ASN][1000 genomes]
rs11655655	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11658328	0.92[ASN][1000 genomes]
rs11867302	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12309	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12450800	0.87[ASN][1000 genomes]
rs12451547	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12451897	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453334	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12453341	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453343	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453764	0.89[ASN][1000 genomes]
rs12601929	0.87[ASN][1000 genomes]
rs12602514	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12602854	0.87[ASN][1000 genomes]
rs12939682	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12940405	0.89[ASN][1000 genomes]
rs2227319	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227321	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241244	0.92[ASN][1000 genomes]
rs2241245	0.92[ASN][1000 genomes]
rs2270401	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302774	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302776	0.81[ASN][1000 genomes]
rs2302777	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305481	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305482	0.88[ASN][1000 genomes]
rs25645	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087852	0.89[ASN][1000 genomes]
rs34003767	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34342173	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34453912	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34540281	0.87[ASN][1000 genomes]
rs34648856	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34933056	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35272691	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35982947	0.87[ASN][1000 genomes]
rs36071767	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3744245	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3785550	0.88[ASN][1000 genomes]
rs3816472	0.91[ASN][1000 genomes]
rs3859187	0.92[ASN][1000 genomes]
rs3859189	0.89[ASN][1000 genomes]
rs3935281	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4065321	0.91[ASN][1000 genomes]
rs4072639	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4433838	0.91[ASN][1000 genomes]
rs66826786	0.88[ASN][1000 genomes]
rs7502971	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8066582	0.92[ASN][1000 genomes]
rs8070444	0.92[ASN][1000 genomes]
rs8071037	0.92[ASN][1000 genomes]
rs8073254	0.92[ASN][1000 genomes]
rs8075668	0.89[ASN][1000 genomes]
rs9898547	0.88[ASN][1000 genomes]
rs9915252	0.91[ASN][1000 genomes]
rs9916158	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2227333	GSDMA	cis	Esophagus Muscularis	GTEx
rs2227333	GSDMA	cis	Nerve Tibial	GTEx
rs2227333	GSDMA	cis	Adipose Subcutaneous	GTEx
rs2227333	MED24	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38166800-38174600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:38167000-38174800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr17:38169600-38175000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr17:38169800-38175600	Enhancers	Fetal Lung	lung
8	chr17:38169800-38176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:38170000-38174200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:38170000-38174600	Enhancers	Fetal Muscle Leg	muscle
11	chr17:38170000-38175200	Weak transcription	Brain Angular Gyrus	brain
12	chr17:38170000-38175600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr17:38170000-38176000	Enhancers	Ovary	ovary
14	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr17:38170200-38174400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr17:38170200-38174600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr17:38170200-38175400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:38170200-38175600	Weak transcription	Brain Substantia Nigra	brain
19	chr17:38170200-38175800	Weak transcription	Primary B cells from cord blood	blood
20	chr17:38170400-38174200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr17:38170400-38174200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr17:38170400-38174200	Enhancers	Stomach Smooth Muscle	stomach
23	chr17:38170400-38174600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr17:38170400-38175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr17:38170400-38175200	Weak transcription	Fetal Brain Male	brain
26	chr17:38170400-38175200	Weak transcription	Dnd41	blood
27	chr17:38170400-38177600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr17:38171000-38174200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr17:38171000-38174200	Weak transcription	NHDF-Ad	bronchial
31	chr17:38171000-38174400	Weak transcription	Esophagus	oesophagus
32	chr17:38171000-38174600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr17:38171000-38175200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:38171200-38175600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:38171400-38174200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr17:38171400-38174200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr17:38171400-38174400	Weak transcription	NH-A	brain
38	chr17:38171400-38174600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
40	chr17:38171600-38174200	Weak transcription	A549	lung
41	chr17:38171600-38175200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr17:38171600-38176800	Weak transcription	Hela-S3	cervix
43	chr17:38171800-38174200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr17:38171800-38174400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:38171800-38175200	Weak transcription	Fetal Thymus	thymus
46	chr17:38172000-38174200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr17:38172000-38174200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr17:38172000-38174200	Weak transcription	Placenta	Placenta
49	chr17:38172000-38175000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr17:38172000-38175600	Weak transcription	GM12878-XiMat	blood

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