Variant report

Variant	rs10799326
Chromosome Location	chr1:226009918-226009919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225998808..226002827-chr1:226008223..226011228,3	MCF-7	breast:
2	chr1:226004660..226006754-chr1:226008430..226011315,2	K562	blood:
3	chr1:226009795..226012080-chr1:226012833..226016826,4	MCF-7	breast:
4	chr1:226004025..226006566-chr1:226007208..226010297,4	MCF-7	breast:
5	chr1:226008498..226011675-chr1:226013682..226016891,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143819	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1011382	0.86[MEX][hapmap]
rs10753410	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038486	0.86[MEX][hapmap]
rs12403480	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3738043	0.91[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs3753661	0.91[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs3766934	0.91[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv947519	chr1:225998770-226034631	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10799326	SLC30A10	cis	cerebellum	SCAN
rs10799326	MIA3	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226000000-226019400	Weak transcription	Fetal Brain Female	brain
2	chr1:226000400-226015800	Enhancers	Ovary	ovary
3	chr1:226001800-226010200	Enhancers	HepG2	liver
4	chr1:226001800-226019200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:226005600-226012000	Weak transcription	Fetal Intestine Large	intestine
6	chr1:226005600-226019400	Weak transcription	Brain Germinal Matrix	brain
7	chr1:226005800-226010400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:226005800-226011600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:226005800-226012000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:226005800-226012400	Weak transcription	Placenta	Placenta
11	chr1:226005800-226013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:226005800-226013400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:226005800-226019200	Weak transcription	NHLF	lung
14	chr1:226005800-226019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:226005800-226019400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:226006000-226011200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:226006200-226010400	Genic enhancers	A549	lung
18	chr1:226006200-226011200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:226006200-226013200	Weak transcription	HSMMtube	muscle
20	chr1:226006200-226013600	Weak transcription	Small Intestine	intestine
21	chr1:226006200-226016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:226006200-226019400	Weak transcription	HSMM	muscle
23	chr1:226006200-226022000	Weak transcription	NHDF-Ad	bronchial
24	chr1:226006400-226010400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:226006400-226010400	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:226006400-226010400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:226006400-226010400	Weak transcription	Esophagus	oesophagus
28	chr1:226006400-226010400	Weak transcription	Gastric	stomach
29	chr1:226006400-226010400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:226006400-226010600	Weak transcription	Lung	lung
31	chr1:226006400-226011000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:226006400-226011200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:226006400-226011200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:226006400-226011200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:226006400-226011400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:226006400-226011400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:226006400-226011600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:226006400-226011600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:226006400-226011800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:226006400-226012000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:226006400-226012600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:226006400-226013000	Weak transcription	Osteobl	bone
43	chr1:226006400-226014200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:226006400-226014800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:226006400-226016800	Weak transcription	Colonic Mucosa	Colon
46	chr1:226006400-226018600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:226006400-226019400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:226006400-226019600	Weak transcription	Hela-S3	cervix
49	chr1:226006600-226010200	Weak transcription	Brain Substantia Nigra	brain
50	chr1:226006600-226010400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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