Variant report

Variant	rs12415272
Chromosome Location	chr10:99472710-99472711
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr10:99472582-99475098	HCT-116	colon:	n/a	n/a
2	MXI1	chr10:99472608-99474975	SK-N-SH	brain:	n/a	n/a
3	MAX	chr10:99472699-99475009	A549	lung:	n/a	n/a
4	POLR2A	chr10:99472694-99475894	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr10:99472311-99472728	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr10:99472651-99475266	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr10:99472591-99480580	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr10:99472621-99475647	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr10:99471308-99485768	MCF10A-Er-Src	breast:	n/a	n/a
10	MAX	chr10:99472639-99475185	HCT-116	colon:	n/a	n/a
11	MAZ	chr10:99472682-99475469	IMR90	lung:	n/a	n/a
12	POLR2A	chr10:99472612-99475161	HUVEC	blood vessel:	n/a	n/a
13	GTF2F1	chr10:99472699-99472817	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr10:99472664-99475455	IMR90	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99471547..99474270-chr10:99495747..99497533,2	K562	blood:
2	chr10:99472472..99476089-chr10:99494153..99498366,9	MCF-7	breast:
3	chr10:99443080..99453237-chr10:99471420..99478243,12	MCF-7	breast:
4	chr10:99472128..99477527-chr10:99495091..99498402,11	MCF-7	breast:
5	chr10:99442762..99448311-chr10:99470830..99475549,8	MCF-7	breast:
6	chr10:99444910..99448624-chr10:99472151..99475238,4	K562	blood:
7	chr10:99446266..99448824-chr10:99470047..99473651,4	K562	blood:

No data

Variant related genes	Relation type
MARVELD1	TF binding region
ENSG00000119986	Chromatin interaction
ENSG00000155256	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10748706	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11189342	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4593946	0.83[LWK][hapmap];0.82[MKK][hapmap]
rs4919133	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4919135	0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6584147	0.85[CEU][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6584148	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6584149	0.95[CHB][hapmap];0.92[CHD][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7896853	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7899948	0.85[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7900119	0.95[CHB][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7914697	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7915100	0.95[CHB][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs946779	0.82[YRI][hapmap]

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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3438921	chr10:99472487-99475335	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12415272	C10orf62	cis	cerebellum	SCAN
rs12415272	DHDPSL	cis	cerebellum	SCAN
rs12415272	SFRP5	cis	cerebellum	SCAN
rs12415272	PI4K2A	cis	parietal	SCAN
rs12415272	PI4K2A	cis	cerebellum	SCAN
rs12415272	FRAT2	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99462000-99472800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:99468400-99472800	Weak transcription	Liver	Liver
3	chr10:99469400-99472800	Weak transcription	Dnd41	blood
4	chr10:99469400-99472800	Weak transcription	K562	blood
5	chr10:99469600-99472800	Weak transcription	Aorta	Aorta
6	chr10:99469600-99472800	Weak transcription	Brain Substantia Nigra	brain
7	chr10:99469600-99472800	Weak transcription	Fetal Intestine Large	intestine
8	chr10:99469600-99472800	Weak transcription	Left Ventricle	heart
9	chr10:99469800-99472800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:99469800-99472800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:99469800-99472800	Weak transcription	Right Ventricle	heart
12	chr10:99469800-99472800	Weak transcription	HSMMtube	muscle
13	chr10:99470000-99472800	Weak transcription	HSMM	muscle
14	chr10:99471400-99472800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr10:99471400-99472800	Enhancers	NHDF-Ad	bronchial
16	chr10:99471400-99473000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr10:99471400-99473000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr10:99471600-99472800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:99471600-99472800	Enhancers	Adipose Nuclei	Adipose
20	chr10:99471600-99472800	Enhancers	Fetal Muscle Trunk	muscle
21	chr10:99471600-99473000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:99471600-99473000	Enhancers	Placenta	Placenta
23	chr10:99471800-99472800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr10:99471800-99473000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr10:99472000-99472800	Enhancers	Fetal Heart	heart
26	chr10:99472000-99472800	Enhancers	Gastric	stomach
27	chr10:99472000-99472800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr10:99472000-99472800	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr10:99472000-99472800	Weak transcription	Right Atrium	heart
30	chr10:99472000-99473000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:99472000-99473400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr10:99472000-99474800	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr10:99472400-99472800	Enhancers	Fetal Muscle Leg	muscle
34	chr10:99472400-99473000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr10:99472400-99473000	Bivalent Enhancer	Primary B cells from cord blood	blood
36	chr10:99472400-99473000	Enhancers	Lung	lung
37	chr10:99472400-99473000	Enhancers	Spleen	Spleen
38	chr10:99472600-99472800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr10:99472600-99472800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr10:99472600-99472800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:99472600-99472800	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr10:99472600-99472800	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr10:99472600-99472800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr10:99472600-99472800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr10:99472600-99472800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr10:99472600-99472800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr10:99472600-99472800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr10:99472600-99472800	Enhancers	Primary hematopoietic stem cells	blood
49	chr10:99472600-99472800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr10:99472600-99472800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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