Variant report

Variant	rs11121572
Chromosome Location	chr1:10517273-10517274
allele	C/T
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	chr1:10516646-10517434	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:10516741-10517274	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:10515583-10517311	K562	blood:	n/a	n/a
4	POLR2A	chr1:10516749-10517533	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:10516757-10517468	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:10516888-10517435	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:10516851-10518561	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:10516682-10517363	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr1:10516678-10517534	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr1:10516988-10517371	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10515344..10518157-chr1:10557483..10560138,2	MCF-7	breast:
2	chr1:10508493..10514342-chr1:10516490..10519388,5	K562	blood:

Variant related genes	Relation type
ENSG00000203469	TF binding region
ENSG00000241563	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];0.86[EUR][1000 genomes]
rs12126556	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12134590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745969	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35138970	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3828044	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6662684	0.87[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
rs11121572	PGD	cis	Muscle Skeletal	GTEx

Chromatin state (count:111 , 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	chr1:10491800-10520600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:10492000-10521200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:10494200-10518800	Weak transcription	K562	blood
16	chr1:10494200-10521400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:10495400-10519000	Weak transcription	Placenta	Placenta
18	chr1:10499200-10531400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:10499400-10519200	Weak transcription	HepG2	liver
20	chr1:10499600-10518200	Weak transcription	Primary B cells from cord blood	blood
21	chr1:10500800-10522800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:10501200-10519200	Weak transcription	Liver	Liver
23	chr1:10501200-10521400	Weak transcription	Brain Angular Gyrus	brain
24	chr1:10503400-10518000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:10503800-10518200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:10505200-10519200	Weak transcription	Hela-S3	cervix
27	chr1:10505200-10520600	Weak transcription	Lung	lung
28	chr1:10505400-10518000	Weak transcription	Dnd41	blood
29	chr1:10508800-10521200	Weak transcription	Pancreas	Pancrea
30	chr1:10509800-10521400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:10510600-10518000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:10510600-10521200	Weak transcription	Gastric	stomach
33	chr1:10510600-10521400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:10510600-10531600	Weak transcription	Right Atrium	heart
35	chr1:10511200-10521200	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:10511200-10522000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:10511400-10522400	Weak transcription	Fetal Kidney	kidney
38	chr1:10511600-10518000	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:10511600-10518200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:10511600-10521200	Weak transcription	Psoas Muscle	Psoas
41	chr1:10511600-10521400	Weak transcription	Brain Anterior Caudate	brain
42	chr1:10511600-10531600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr1:10511800-10517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:10511800-10517800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:10511800-10519000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:10511800-10519600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:10511800-10521200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:10511800-10521200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:10511800-10521400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:10512000-10517800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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