Variant report

Variant	rs11587288
Chromosome Location	chr1:171770239-171770240
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	POLR2A	chr1:171770160-171770286	HepG2	liver:	n/a	n/a
2	CTCF	chr1:171770140-171770290	GM12873	blood:	n/a	n/a
3	CTCF	chr1:171770174-171771278	SK-N-SH	brain:	n/a	chr1:171770733-171770741 chr1:171770299-171770320 chr1:171770730-171770751 chr1:171770728-171770746 chr1:171770729-171770745
4	CTCF	chr1:171770180-171770330	BE2_C	brain:	n/a	chr1:171770299-171770320
5	CTCF	chr1:171770140-171770290	HRE	kidney:	n/a	n/a
6	CTCF	chr1:171770160-171770310	HPF	lung:	n/a	n/a
7	CTCF	chr1:171770200-171770350	GM12872	blood:	n/a	chr1:171770299-171770320
8	POLR2A	chr1:171769990-171770784	GM12878	blood:	n/a	n/a
9	CTCF	chr1:171770147-171771845	A549	lung:	n/a	chr1:171770733-171770741 chr1:171770299-171770320 chr1:171770730-171770751 chr1:171770728-171770746 chr1:171770729-171770745
10	CTCF	chr1:171770100-171770250	HCFaa	heart:	n/a	n/a
11	CTCF	chr1:171770220-171770370	AG09309	skin:	n/a	chr1:171770299-171770320
12	RAD21	chr1:171770002-171771149	SK-N-SH	brain:	n/a	chr1:171770574-171770583 chr1:171770308-171770317 chr1:171770729-171770748 chr1:171770731-171770738

No.	Distal block	Cell Line	Cell type
1	chr1:171768938..171770911-chr1:171953198..171954740,2	MCF-7	breast:
2	chr1:171769381..171771260-chr1:171953518..171955015,12	MCF-7	breast:
3	chr1:171769639..171771616-chr1:171952138..171953508,27	MCF-7	breast:
4	chr1:171770037..171771242-chr1:171953555..171955020,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213060	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10489253	0.83[YRI][hapmap]
rs10798636	0.84[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs10798667	0.92[ASN][1000 genomes]
rs10798692	0.94[MEX][hapmap]
rs10913644	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11590059	0.83[AFR][1000 genomes]
rs11803889	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs12022693	0.83[AFR][1000 genomes]
rs12034454	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12039034	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12566700	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs16843385	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17597528	0.83[AFR][1000 genomes]
rs2206541	0.83[YRI][hapmap]
rs2232812	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232816	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2232818	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2232826	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294717	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294723	0.94[MEX][hapmap]
rs3753538	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56167663	0.83[AFR][1000 genomes]
rs56178029	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57476157	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59302445	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60502293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60956160	0.87[EUR][1000 genomes]
rs6425423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425428	0.83[AFR][1000 genomes]
rs6425438	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs6425439	0.91[ASN][1000 genomes]
rs6684594	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6691222	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6695502	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700184	0.86[YRI][hapmap]
rs72703115	0.92[ASN][1000 genomes]
rs7537770	0.83[YRI][hapmap]
rs7541192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7543608	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7548462	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7556602	0.89[YRI][hapmap]
rs7860	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909958	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs941942	0.84[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11587288	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs11587288	METTL13	cis	parietal	SCAN
rs11587288	DNM3	cis	cerebellum	SCAN
rs11587288	MAEL	cis	parietal	SCAN
rs11587288	BAT2L2	cis	parietal	SCAN
rs11587288	ILDR2	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:171763800-171770400	Weak transcription	Small Intestine	intestine
4	chr1:171765000-171774600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:171765600-171770800	Weak transcription	Hela-S3	cervix
6	chr1:171766000-171772800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:171766000-171774800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:171766200-171774400	Weak transcription	Brain Substantia Nigra	brain
9	chr1:171766200-171774600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:171766200-171774600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:171766200-171775400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:171766200-171777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:171766400-171777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:171766600-171770800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:171766600-171774600	Weak transcription	Ovary	ovary
16	chr1:171766600-171774800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:171766600-171774800	Weak transcription	Placenta	Placenta
18	chr1:171766600-171774800	Weak transcription	HepG2	liver
19	chr1:171766800-171770400	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:171766800-171770400	Weak transcription	Fetal Kidney	kidney
21	chr1:171766800-171771800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:171766800-171772800	Weak transcription	Right Ventricle	heart
23	chr1:171766800-171774600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:171766800-171774600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:171767000-171770400	Weak transcription	Brain Angular Gyrus	brain
26	chr1:171767000-171770800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:171767000-171770800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:171767000-171771600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:171767000-171774600	Weak transcription	K562	blood
30	chr1:171767000-171774800	Weak transcription	Osteobl	bone
31	chr1:171767000-171777200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:171767000-171778600	Weak transcription	NHEK	skin
33	chr1:171767200-171774600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:171767200-171774800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:171767200-171774800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:171767200-171777600	Weak transcription	HMEC	breast
37	chr1:171767400-171770400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:171767400-171770800	Weak transcription	A549	lung
39	chr1:171767400-171771000	Weak transcription	Fetal Brain Female	brain
40	chr1:171767400-171771400	Weak transcription	NHLF	lung
41	chr1:171767400-171771600	Weak transcription	Dnd41	blood
42	chr1:171767400-171773600	Weak transcription	HUVEC	blood vessel
43	chr1:171767400-171774600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr1:171767400-171774800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:171767400-171774800	Weak transcription	Psoas Muscle	Psoas
46	chr1:171767400-171775000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:171767400-171777200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:171767600-171770800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:171767600-171772000	Weak transcription	Lung	lung
50	chr1:171767600-171774800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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