Variant report

Variant	rs2236582
Chromosome Location	chr6:109765818-109765819
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:109765747-109766609	K562	blood:	n/a	n/a
2	POLR2A	chr6:109764767-109765844	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr6:109765770-109771599	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:109765785-109766180	K562	blood:	n/a	n/a
5	POLR2A	chr6:109765681-109771914	GM12892	blood:	n/a	n/a
6	POLR2A	chr6:109765710-109771793	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:109763209-109771395	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr6:109765798-109766393	K562	blood:	n/a	n/a
9	POLR2A	chr6:109761500-109772072	GM12892	blood:	n/a	n/a
10	POLR2A	chr6:109761656-109772338	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:109761808-109772355	GM12891	blood:	n/a	n/a
12	POLR2A	chr6:109763255-109772269	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:109739441..109742103-chr6:109765700..109768387,2	MCF-7	breast:
2	chr6:109764530..109766922-chr6:109796354..109798276,2	K562	blood:
3	chr6:109765568..109767233-chr6:109789401..109791135,2	MCF-7	breast:
4	chr6:109764918..109767515-chr6:109797927..109799949,2	MCF-7	breast:
5	chr6:109701746..109704787-chr6:109765536..109768393,4	K562	blood:
6	chr6:109701777..109705568-chr6:109765713..109769272,5	K562	blood:
7	chr6:109764609..109767226-chr6:109791352..109794243,2	K562	blood:

No data

Variant related genes	Relation type
PPIL6	TF binding region
ENSG00000260273	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10080429	0.94[EUR][1000 genomes]
rs1040284	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10457190	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10457194	0.86[CHB][hapmap]
rs10457195	0.86[CHB][hapmap]
rs1048203	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499053	0.90[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs10782161	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10782162	0.90[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10872032	0.91[EUR][1000 genomes]
rs10872034	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11153171	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11153174	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11153175	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11153176	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11153177	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153180	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153181	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153183	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs11251	0.85[MKK][hapmap]
rs11753645	0.84[CEU][hapmap]
rs11754455	0.85[CHB][hapmap]
rs11755641	0.86[CHB][hapmap]
rs11967108	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12190920	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12190996	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12192847	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12193493	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12194061	0.86[CHB][hapmap]
rs12197114	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12197180	0.86[CHB][hapmap]
rs12198938	0.86[CHB][hapmap]
rs12199154	0.86[CHB][hapmap]
rs12206928	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12208933	0.90[CEU][hapmap];0.80[CHB][hapmap]
rs12209691	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12212476	0.86[CHB][hapmap]
rs12213313	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12524273	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12524639	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12528712	0.80[CEU][hapmap]
rs12528822	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13195517	0.80[CEU][hapmap]
rs13199519	0.84[CEU][hapmap]
rs13203252	0.84[CEU][hapmap]
rs13212766	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13220915	0.86[CHB][hapmap]
rs1322816	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1358997	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1358998	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1406899	0.86[CHB][hapmap]
rs1546980	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1590306	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17070580	0.90[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs1923725	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980591	0.85[CHB][hapmap]
rs2024850	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs2275650	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2277114	0.86[CHB][hapmap]
rs34202013	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35056702	0.95[EUR][1000 genomes]
rs36035949	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36099706	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3757234	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778475	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778477	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799835	0.80[CEU][hapmap]
rs3799839	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3807005	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818934	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59056467	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59906308	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68042406	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6911838	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs6914498	0.89[CEU][hapmap];0.80[CHB][hapmap]
rs6920962	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6929023	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs729888	0.86[CHB][hapmap]
rs7372	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs752262	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7754650	0.80[ASW][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap]
rs7755941	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs7773095	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7773950	0.86[CHB][hapmap]
rs9320287	0.90[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs9480933	0.90[EUR][1000 genomes]
rs9480948	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9480951	0.95[EUR][1000 genomes]
rs9480953	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs9480955	0.95[EUR][1000 genomes]
rs9480957	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9487068	0.93[EUR][1000 genomes]
rs9487094	0.90[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs9487095	0.95[EUR][1000 genomes]
rs9487097	0.90[EUR][1000 genomes]
rs9487098	0.92[EUR][1000 genomes]
rs9487100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9885646	0.90[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2236582	SMPD2	cis	multi-tissue	Pritchard
rs2236582	PDSS2	cis	cerebellum	SCAN
rs2236582	AKD1	cis	cerebellum	SCAN
rs2236582	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs2236582	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs2236582	MICAL1	cis	parietal	SCAN
rs2236582	SMPD2	cis	parietal	SCAN
rs2236582	SMPD2	cis	cerebellum	SCAN
rs2236582	SMPD2	cis	Whole Blood	GTEx
rs2236582	PPIL6	cis	brain	seeQTL
rs2236582	CD164	cis	parietal	SCAN
rs2236582	PPIL6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109762800-109775800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:109763200-109774400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:109763200-109775600	Weak transcription	Fetal Kidney	kidney
4	chr6:109763200-109775800	Weak transcription	HUVEC	blood vessel
5	chr6:109763400-109766000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:109763400-109766200	Genic enhancers	Esophagus	oesophagus
7	chr6:109763400-109766400	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr6:109763400-109768600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:109763400-109770400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:109763400-109775000	Strong transcription	NHLF	lung
11	chr6:109763400-109775200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:109763600-109766000	Weak transcription	Brain Angular Gyrus	brain
13	chr6:109763600-109767400	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:109763600-109768200	Strong transcription	Fetal Lung	lung
15	chr6:109763600-109768400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:109763600-109768400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:109763600-109768400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:109763600-109768400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:109763600-109768600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:109763600-109768600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:109763600-109768800	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr6:109763600-109768800	Strong transcription	Brain Anterior Caudate	brain
23	chr6:109763600-109769400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:109763600-109769600	Weak transcription	Brain Substantia Nigra	brain
25	chr6:109763600-109770000	Strong transcription	NHEK	skin
26	chr6:109763600-109770800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:109763600-109773200	Weak transcription	Fetal Brain Male	brain
28	chr6:109763600-109775000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:109763600-109775200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:109763600-109775800	Weak transcription	Right Atrium	heart
31	chr6:109763800-109767000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:109763800-109767200	Strong transcription	Rectal Smooth Muscle	rectum
33	chr6:109763800-109768000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:109763800-109768000	Strong transcription	Brain Hippocampus Middle	brain
35	chr6:109763800-109768400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:109763800-109768400	Strong transcription	Liver	Liver
37	chr6:109763800-109769000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:109763800-109769000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:109763800-109769600	Strong transcription	Fetal Muscle Leg	muscle
40	chr6:109763800-109769800	Strong transcription	Thymus	Thymus
41	chr6:109763800-109770600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:109763800-109770600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:109763800-109770800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:109763800-109771000	Strong transcription	Fetal Intestine Small	intestine
45	chr6:109763800-109774400	Strong transcription	HSMM	muscle
46	chr6:109763800-109774600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:109763800-109774800	Strong transcription	Fetal Stomach	stomach
48	chr6:109763800-109774800	Weak transcription	Small Intestine	intestine
49	chr6:109763800-109775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:109763800-109775400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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