Variant report

Variant	rs12134590
Chromosome Location	chr1:10516290-10516291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:52)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:52 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:10516205-10516442	HepG2	liver:	n/a	n/a
2	CTCF	chr1:10516260-10516410	HEK293	kidney:	n/a	n/a
3	CTCF	chr1:10516240-10516390	HMEC	breast:	n/a	n/a
4	CTCF	chr1:10516220-10516370	HRE	kidney:	n/a	n/a
5	ZNF143	chr1:10516277-10516444	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:10516138-10516457	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr1:10516237-10516443	GM12892	blood:	n/a	n/a
8	RAD21	chr1:10516070-10516513	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr1:10516244-10516437	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr1:10516277-10516354	K562	blood:	n/a	n/a
11	CTCF	chr1:10516180-10516330	HMEC	breast:	n/a	n/a
12	CTCF	chr1:10516257-10516425	HepG2	liver:	n/a	n/a
13	CTCF	chr1:10516260-10516410	SK-N-SH_RA	brain:	n/a	n/a
14	CTCF	chr1:10516280-10516430	GM12878	blood:	n/a	n/a
15	RAD21	chr1:10516145-10516423	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr1:10516280-10516430	HBMEC	blood vessel:	n/a	n/a
17	CTCF	chr1:10516260-10516410	GM12874	blood:	n/a	n/a
18	POLR2A	chr1:10516167-10516462	K562	blood:	n/a	n/a
19	POLR2A	chr1:10516144-10516481	K562	blood:	n/a	n/a
20	CTCF	chr1:10516220-10516370	GM12866	blood:	n/a	n/a
21	CTCF	chr1:10516220-10516370	GM12872	blood:	n/a	n/a
22	POLR2A	chr1:10516254-10516297	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:10515583-10517311	K562	blood:	n/a	n/a
24	POLR2A	chr1:10516278-10516434	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr1:10516280-10516430	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:10516095-10516331	K562	blood:	n/a	n/a
27	CTCF	chr1:10516200-10516350	HEEpiC	esophagus:	n/a	n/a
28	CTCF	chr1:10516240-10516390	HMF	breast:	n/a	n/a
29	RAD21	chr1:10516222-10516461	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr1:10516240-10516390	AG04449	skin:	n/a	n/a
31	POLR2A	chr1:10515722-10516546	PANC-1	pancreas:	n/a	n/a
32	CTCF	chr1:10516240-10516390	MCF-7	breast:	n/a	n/a
33	CTCF	chr1:10516145-10516447	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr1:10516240-10516390	GM12864	blood:	n/a	n/a
35	CTCF	chr1:10516240-10516390	HPAF	blood vessel:	n/a	n/a
36	CTCF	chr1:10516260-10516410	NHEK	skin:	n/a	n/a
37	CTCF	chr1:10516280-10516430	NHEK	skin:	n/a	n/a
38	CTCF	chr1:10516260-10516410	GM12870	blood:	n/a	n/a
39	POLR2A	chr1:10516187-10516326	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr1:10516260-10516410	HPAF	blood vessel:	n/a	n/a
41	CTCF	chr1:10516220-10516370	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:10516229-10516388	K562	blood:	n/a	n/a
43	POLR2A	chr1:10516056-10516498	PANC-1	pancreas:	n/a	n/a
44	CTCF	chr1:10516206-10516442	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr1:10516282-10516323	GM12878	blood:	n/a	n/a
46	CTCF	chr1:10516280-10516430	SAEC	small airway:	n/a	n/a
47	CTCF	chr1:10516200-10516350	K562	blood:	n/a	n/a
48	CTCF	chr1:10516280-10516430	HCPEpiC	choroid plexus:	n/a	n/a
49	CTCF	chr1:10516255-10516420	NHEK	skin:	n/a	n/a
50	CTCF	chr1:10516220-10516370	WERI-Rb-1	eye:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10514752..10516295-chr1:10530439..10532532,2	K562	blood:
2	chr1:10515344..10518157-chr1:10557483..10560138,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203469	TF binding region
ENSG00000142655	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10436981	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11121572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126556	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12745969	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35138970	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3828044	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6662684	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers 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 miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12134590	PGD	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10491400-10519000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:10491400-10521000	Weak transcription	Ovary	ovary
3	chr1:10491400-10521200	Weak transcription	Aorta	Aorta
4	chr1:10491600-10517800	Weak transcription	Primary T cells from cord blood	blood
5	chr1:10491600-10518000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:10491600-10518000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:10491600-10519200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:10491600-10521200	Weak transcription	Brain Substantia Nigra	brain
9	chr1:10491600-10521200	Weak transcription	Left Ventricle	heart
10	chr1:10491600-10521200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:10491600-10521200	Weak transcription	Spleen	Spleen
12	chr1:10491600-10521400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:10491800-10516600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:10491800-10516600	Weak transcription	HSMM	muscle
15	chr1:10491800-10520600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:10492000-10521200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:10492400-10517200	Weak transcription	Brain Germinal Matrix	brain
18	chr1:10493600-10516800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:10494200-10518800	Weak transcription	K562	blood
20	chr1:10494200-10521400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:10495400-10519000	Weak transcription	Placenta	Placenta
22	chr1:10499200-10531400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:10499400-10519200	Weak transcription	HepG2	liver
24	chr1:10499600-10518200	Weak transcription	Primary B cells from cord blood	blood
25	chr1:10500800-10522800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:10501200-10519200	Weak transcription	Liver	Liver
27	chr1:10501200-10521400	Weak transcription	Brain Angular Gyrus	brain
28	chr1:10503400-10518000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:10503800-10518200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:10505200-10519200	Weak transcription	Hela-S3	cervix
31	chr1:10505200-10520600	Weak transcription	Lung	lung
32	chr1:10505400-10518000	Weak transcription	Dnd41	blood
33	chr1:10507400-10517000	Weak transcription	A549	lung
34	chr1:10508800-10521200	Weak transcription	Pancreas	Pancrea
35	chr1:10509800-10521400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:10510600-10518000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:10510600-10521200	Weak transcription	Gastric	stomach
38	chr1:10510600-10521400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:10510600-10531600	Weak transcription	Right Atrium	heart
40	chr1:10511200-10521200	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:10511200-10522000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:10511400-10522400	Weak transcription	Fetal Kidney	kidney
43	chr1:10511600-10518000	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:10511600-10518200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:10511600-10521200	Weak transcription	Psoas Muscle	Psoas
46	chr1:10511600-10521400	Weak transcription	Brain Anterior Caudate	brain
47	chr1:10511600-10531600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr1:10511800-10516400	Weak transcription	Fetal Heart	heart
49	chr1:10511800-10516600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:10511800-10516800	Weak transcription	Rectal Mucosa Donor 29	rectum

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