Variant report

Variant	rs7522582
Chromosome Location	chr1:171770111-171770112
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	POLR2A	chr1:171770034-171770193	MCF-7	breast:	n/a	n/a
2	CTCF	chr1:171770000-171770150	HMEC	breast:	n/a	n/a
3	POLR2A	chr1:171769990-171770784	GM12878	blood:	n/a	n/a
4	CTCF	chr1:171770100-171770250	HCFaa	heart:	n/a	n/a
5	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	chr1:171769328..171770170-chr1:171952653..171953200,2	MCF-7	breast:
3	chr1:171769381..171771260-chr1:171953518..171955015,12	MCF-7	breast:
4	chr1:171769639..171771616-chr1:171952138..171953508,27	MCF-7	breast:
5	chr1:171768042..171770155-chr1:171772867..171774422,2	MCF-7	breast:
6	chr1:171770037..171771242-chr1:171953555..171955020,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213060	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1045456	0.94[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]
rs10489252	0.94[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12091786	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]
rs12565176	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs12567851	0.87[EUR][1000 genomes]
rs12730717	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12742601	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750330	0.88[EUR][1000 genomes]
rs12753043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17596025	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs17596081	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs17649609	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs17650310	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17650340	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657363	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1801898	0.94[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]
rs2143369	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181216	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs2223602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2232807	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232813	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232819	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232824	0.94[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]
rs2232825	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294718	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236894	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs236897	0.86[EUR][1000 genomes]
rs236898	0.86[EUR][1000 genomes]
rs236899	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs236900	0.87[EUR][1000 genomes]
rs236907	0.94[CEU][hapmap]
rs34320898	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34627492	0.88[EUR][1000 genomes]
rs35249022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400839	0.99[EUR][1000 genomes]
rs35631282	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35674909	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35882887	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35930163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36080557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891278	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55732843	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56365362	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56377810	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61807979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656852	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674364	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs6675708	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs6681322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6687624	0.90[JPT][hapmap]
rs6689125	0.94[EUR][1000 genomes]
rs6695933	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7536142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7522582	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 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	chr1:171752800-171770200	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr1:171754200-171770200	Strong transcription	Primary T cells from cord blood	blood
5	chr1:171754200-171770200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:171763800-171770400	Weak transcription	Small Intestine	intestine
7	chr1:171765000-171774600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:171765600-171770800	Weak transcription	Hela-S3	cervix
9	chr1:171766000-171772800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:171766000-171774800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:171766200-171774400	Weak transcription	Brain Substantia Nigra	brain
12	chr1:171766200-171774600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:171766200-171774600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:171766200-171775400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:171766200-171777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:171766400-171770200	Weak transcription	NH-A	brain
17	chr1:171766400-171777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:171766600-171770200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:171766600-171770800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:171766600-171774600	Weak transcription	Ovary	ovary
21	chr1:171766600-171774800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:171766600-171774800	Weak transcription	Placenta	Placenta
23	chr1:171766600-171774800	Weak transcription	HepG2	liver
24	chr1:171766800-171770400	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:171766800-171770400	Weak transcription	Fetal Kidney	kidney
26	chr1:171766800-171771800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:171766800-171772800	Weak transcription	Right Ventricle	heart
28	chr1:171766800-171774600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:171766800-171774600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:171767000-171770400	Weak transcription	Brain Angular Gyrus	brain
31	chr1:171767000-171770800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:171767000-171770800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:171767000-171771600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:171767000-171774600	Weak transcription	K562	blood
35	chr1:171767000-171774800	Weak transcription	Osteobl	bone
36	chr1:171767000-171777200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:171767000-171778600	Weak transcription	NHEK	skin
38	chr1:171767200-171770200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:171767200-171774600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:171767200-171774800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:171767200-171774800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:171767200-171777600	Weak transcription	HMEC	breast
43	chr1:171767400-171770200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:171767400-171770200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:171767400-171770400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:171767400-171770800	Weak transcription	A549	lung
47	chr1:171767400-171771000	Weak transcription	Fetal Brain Female	brain
48	chr1:171767400-171771400	Weak transcription	NHLF	lung
49	chr1:171767400-171771600	Weak transcription	Dnd41	blood
50	chr1:171767400-171773600	Weak transcription	HUVEC	blood vessel

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