Variant report

Variant	rs12591197
Chromosome Location	chr15:35263640-35263641
allele	A/C
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	chr15:35263463-35263654	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:35261639..35264057-chr15:35280199..35283795,4	MCF-7	breast:
2	chr15:35263427..35267661-chr15:35274185..35276277,3	MCF-7	breast:
3	chr15:35260342..35263784-chr15:35278927..35282487,7	K562	blood:
4	chr15:35263307..35266345-chr15:35268567..35270938,3	K562	blood:

Variant related genes	Relation type
AQR	TF binding region
ENSG00000212768	Chromatin interaction
ENSG00000198146	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10438394	0.90[ASN][1000 genomes]
rs11073076	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11629721	0.88[ASN][1000 genomes]
rs11635485	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11636350	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12439825	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12441204	0.83[ASN][1000 genomes]
rs12442577	0.84[EUR][1000 genomes]
rs12442905	0.90[ASN][1000 genomes]
rs12593603	0.90[ASN][1000 genomes]
rs12595318	0.81[ASN][1000 genomes]
rs12708534	0.93[ASN][1000 genomes]
rs12901394	0.90[ASN][1000 genomes]
rs12901466	0.90[ASN][1000 genomes]
rs12901794	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12915053	0.84[ASN][1000 genomes]
rs2060809	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2060810	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2060811	0.95[ASN][1000 genomes]
rs2060812	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2305411	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28498500	0.90[ASN][1000 genomes]
rs28715915	0.82[ASN][1000 genomes]
rs36067547	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4513050	0.94[ASN][1000 genomes]
rs4923845	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4923849	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6495728	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6495729	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6495730	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7164151	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7164169	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7164266	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7170280	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7172507	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7177337	0.95[ASN][1000 genomes]
rs7179205	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7179833	0.94[ASN][1000 genomes]
rs7181836	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7182356	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8031861	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8037610	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9920236	0.84[ASN][1000 genomes]
rs9920529	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3350109	chr15:34668106-35534229	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv522411	chr15:34953986-35462981	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2761865	chr15:35101678-35271639	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv832967	chr15:35110102-35267906	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12591197	ENSG00000021776	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:35262000-35276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:35262000-35278600	Weak transcription	Gastric	stomach
3	chr15:35262400-35265600	Weak transcription	Fetal Heart	heart
4	chr15:35262400-35269600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:35262400-35269600	Weak transcription	HSMM	muscle
6	chr15:35262400-35269800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:35262400-35270000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:35262400-35273200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:35262400-35273400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:35262400-35273400	Weak transcription	GM12878-XiMat	blood
11	chr15:35262400-35273600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:35262400-35273600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:35262400-35273600	Weak transcription	Fetal Intestine Large	intestine
14	chr15:35262400-35273600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:35262400-35274600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:35262400-35274600	Weak transcription	NHLF	lung
17	chr15:35262400-35278600	Weak transcription	HSMMtube	muscle
18	chr15:35262400-35279000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:35262400-35279000	Weak transcription	Aorta	Aorta
20	chr15:35262600-35264000	Weak transcription	Fetal Brain Female	brain
21	chr15:35262600-35264400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:35262600-35264400	Weak transcription	K562	blood
23	chr15:35262600-35265600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:35262600-35265600	Weak transcription	HUVEC	blood vessel
25	chr15:35262600-35267400	Weak transcription	Brain Anterior Caudate	brain
26	chr15:35262600-35268400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:35262600-35269000	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:35262600-35269200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:35262600-35269600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:35262600-35269800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:35262600-35269800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:35262600-35269800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr15:35262600-35270000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:35262600-35270200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:35262600-35271000	Weak transcription	Fetal Thymus	thymus
36	chr15:35262600-35271200	Weak transcription	A549	lung
37	chr15:35262600-35272800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:35262600-35273200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr15:35262600-35273200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:35262600-35273200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:35262600-35273400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:35262600-35273400	Weak transcription	Primary T cells from cord blood	blood
43	chr15:35262600-35273400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:35262600-35273400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr15:35262600-35273600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:35262600-35273600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:35262600-35273600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:35262600-35273600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:35262600-35273600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:35262600-35273600	Weak transcription	Liver	Liver

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