Variant report

Variant	rs2305482
Chromosome Location	chr17:38140927-38140928
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38140511-38141321	K562	blood:	n/a	n/a
2	POLR2A	chr17:38140750-38141232	GM12891	blood:	n/a	n/a
3	POLR2A	chr17:38140458-38141255	GM12891	blood:	n/a	n/a
4	POLR2A	chr17:38140342-38141747	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr17:38140460-38141267	K562	blood:	n/a	n/a
6	POLR2A	chr17:38140394-38142008	K562	blood:	n/a	n/a
7	POLR2A	chr17:38140390-38141753	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr17:38140494-38141440	GM12878	blood:	n/a	n/a
9	POLR2A	chr17:38140603-38141068	HepG2	liver:	n/a	n/a
10	POLR2A	chr17:38140886-38141035	K562	blood:	n/a	n/a
11	POLR2A	chr17:38140804-38141345	GM12891	blood:	n/a	n/a
12	POLR2A	chr17:38140617-38141287	GM12892	blood:	n/a	n/a
13	POLR2A	chr17:38140459-38141456	GM12892	blood:	n/a	n/a
14	POLR2A	chr17:38140654-38141322	GM12892	blood:	n/a	n/a
15	POLR2A	chr17:38140731-38140995	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38136187..38139299-chr17:38140015..38144342,5	K562	blood:
2	chr17:38139958..38142841-chr17:38144945..38147813,2	MCF-7	breast:
3	chr17:38139548..38141921-chr17:38833362..38835168,2	K562	blood:
4	chr17:38081395..38083587-chr17:38139253..38141219,2	K562	blood:
5	chr17:38140110..38141671-chr17:38147134..38149344,2	K562	blood:
6	chr17:38139951..38141671-chr17:38146998..38149344,2	K562	blood:
7	chr17:38135505..38137340-chr17:38139696..38141236,2	MCF-7	breast:

No data

Variant related genes	Relation type
PSMD3	TF binding region
ENSG00000108344	Chromatin interaction
ENSG00000172057	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1042658	0.89[YRI][hapmap]
rs1045929	0.89[YRI][hapmap]
rs11078930	0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs11078931	0.92[ASN][1000 genomes]
rs11078935	0.80[ASN][1000 genomes]
rs11078936	0.91[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]
rs11655264	0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11658328	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11867302	0.90[ASN][1000 genomes]
rs12309	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12450688	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12450800	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12451547	0.87[ASN][1000 genomes]
rs12451897	0.87[ASN][1000 genomes]
rs12453249	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12453334	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12453341	0.87[ASN][1000 genomes]
rs12453343	0.87[ASN][1000 genomes]
rs12453764	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12601929	0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs12602514	0.82[ASN][1000 genomes]
rs12940405	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227319	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2227321	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2227322	0.89[YRI][hapmap]
rs2227333	0.88[ASN][1000 genomes]
rs2241244	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241245	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2270401	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2302774	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2302776	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2302777	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2305481	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs25645	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3087852	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3213762	0.85[YRI][hapmap]
rs34342173	0.87[ASN][1000 genomes]
rs34453912	0.86[ASN][1000 genomes]
rs34648856	0.93[ASN][1000 genomes]
rs34933056	0.87[ASN][1000 genomes]
rs35272691	0.89[ASN][1000 genomes]
rs36071767	0.83[ASN][1000 genomes]
rs3744245	0.93[ASN][1000 genomes]
rs3785550	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816472	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3859187	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3859189	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3859192	0.81[MKK][hapmap]
rs3935281	0.82[ASN][1000 genomes]
rs4065321	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4072639	0.82[ASN][1000 genomes]
rs4433838	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs709591	0.89[YRI][hapmap]
rs709592	0.89[YRI][hapmap]
rs7502971	0.84[ASN][1000 genomes]
rs8066582	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8070444	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8071037	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8073254	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8075668	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs8077456	0.84[JPT][hapmap]
rs8078723	0.87[MKK][hapmap];0.85[YRI][hapmap]
rs9898547	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9915252	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9916158	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2305482	SLFN11	cis	parietal	SCAN
rs2305482	GSDMA	cis	Esophagus Muscularis	GTEx
rs2305482	GSDMA	cis	Adipose Subcutaneous	GTEx
rs2305482	MED24	cis	Nerve Tibial	GTEx
rs2305482	MED24	cis	Artery Tibial	GTEx
rs2305482	MED24	cis	parietal	SCAN
rs2305482	MED24	cis	cerebellum	SCAN
rs2305482	PCGF2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38138600-38149200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:38138600-38154200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:38139000-38144400	Weak transcription	Fetal Heart	heart
4	chr17:38139200-38151400	Strong transcription	NHEK	skin
5	chr17:38139200-38154800	Strong transcription	Fetal Intestine Small	intestine
6	chr17:38139400-38141200	Genic enhancers	Dnd41	blood
7	chr17:38139400-38152200	Strong transcription	K562	blood
8	chr17:38139400-38154400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:38139400-38155000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:38139600-38151200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:38139600-38153600	Strong transcription	HUVEC	blood vessel
12	chr17:38139600-38154400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr17:38139600-38154600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr17:38139600-38154800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:38139600-38155000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr17:38139600-38155200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:38139600-38155400	Strong transcription	Placenta	Placenta
18	chr17:38139600-38155600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr17:38139600-38155600	Strong transcription	Fetal Thymus	thymus
20	chr17:38139800-38153800	Strong transcription	Osteobl	bone
21	chr17:38139800-38154400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr17:38139800-38154400	Strong transcription	HMEC	breast
23	chr17:38139800-38154600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr17:38139800-38154600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:38139800-38154800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr17:38139800-38155000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr17:38139800-38155000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr17:38139800-38155000	Strong transcription	A549	lung
29	chr17:38139800-38155600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr17:38140000-38148800	Strong transcription	Liver	Liver
31	chr17:38140000-38150400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr17:38140000-38150400	Strong transcription	Fetal Muscle Leg	muscle
33	chr17:38140000-38151200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr17:38140000-38152400	Strong transcription	Adipose Nuclei	Adipose
35	chr17:38140000-38153800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr17:38140000-38153800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr17:38140000-38154200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr17:38140000-38154200	Strong transcription	Brain Germinal Matrix	brain
39	chr17:38140000-38154200	Strong transcription	Lung	lung
40	chr17:38140000-38154400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr17:38140000-38154400	Strong transcription	Right Ventricle	heart
42	chr17:38140000-38154600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr17:38140000-38154600	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr17:38140000-38154600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:38140000-38154600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr17:38140000-38154600	Strong transcription	Brain Hippocampus Middle	brain
47	chr17:38140000-38154600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr17:38140000-38154600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr17:38140000-38154600	Strong transcription	Fetal Intestine Large	intestine
50	chr17:38140000-38155000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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