Variant report

Variant	rs1932001
Chromosome Location	chr10:99172751-99172752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:99165782..99177128-chr10:99179856..99189832,30	MCF-7	breast:
2	chr10:99170419..99173744-chr10:99178891..99183198,3	MCF-7	breast:
3	chr10:99159566..99161975-chr10:99171116..99175343,4	K562	blood:
4	chr10:99168511..99173804-chr10:99184850..99187816,7	MCF-7	breast:
5	chr10:99166045..99168504-chr10:99170322..99173005,2	K562	blood:
6	chr10:99160204..99163024-chr10:99171580..99174293,2	K562	blood:
7	chr10:99171315..99175453-chr10:99176654..99180468,6	K562	blood:
8	chr10:99171445..99174170-chr10:99204178..99207806,5	MCF-7	breast:
9	chr10:99163386..99166099-chr10:99171495..99174383,2	MCF-7	breast:
10	chr10:99168420..99171279-chr10:99172405..99174703,2	K562	blood:
11	chr10:99166892..99169975-chr10:99170359..99172836,3	MCF-7	breast:
12	chr10:99172474..99176419-chr10:99183924..99185972,3	K562	blood:
13	chr10:99172592..99175425-chr20:52209106..52210731,2	MCF-7	breast:
14	chr10:99172460..99176520-chr10:99201147..99207313,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171940	Chromatin interaction
ENSG00000200737	Chromatin interaction
ENSG00000052749	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000224474	Chromatin interaction
ENSG00000171314	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000231970	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10444014	0.80[AMR][1000 genomes]
rs10444016	0.80[AMR][1000 genomes]
rs10786344	0.83[CEU][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes]
rs10786345	0.81[AMR][1000 genomes]
rs10786346	0.81[AMR][1000 genomes]
rs10786347	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10882929	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10882930	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10882931	0.81[AMR][1000 genomes]
rs11189173	0.81[CEU][hapmap]
rs11189204	0.80[AMR][1000 genomes]
rs11189206	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs11189208	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11189211	0.89[GIH][hapmap];0.86[AMR][1000 genomes]
rs11189214	0.90[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17112674	0.82[GIH][hapmap]
rs2297667	0.82[GIH][hapmap]
rs6584128	0.83[CEU][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes]
rs7078782	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs7895695	0.91[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9887994	0.83[AMR][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	nsv467438	chr10:99126249-99173870	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv552024	chr10:99126249-99173870	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv467440	chr10:99134784-99204791	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv552025	chr10:99134784-99204791	Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1932001	RRP12	cis	cerebellum	SCAN
rs1932001	RRP12	cis	Heart Left Ventricle	GTEx
rs1932001	RRP12	cis	Muscle Skeletal	GTEx
rs1932001	RRP12	cis	parietal	SCAN
rs1932001	MMS19	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99161600-99178800	Weak transcription	Fetal Stomach	stomach
2	chr10:99161600-99185200	Weak transcription	Pancreas	Pancrea
3	chr10:99167400-99174000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:99167400-99174800	Weak transcription	NHDF-Ad	bronchial
5	chr10:99167400-99176200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:99167400-99178000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:99167400-99179000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:99167400-99185200	Weak transcription	Fetal Lung	lung
9	chr10:99167400-99185400	Weak transcription	Gastric	stomach
10	chr10:99167600-99172800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr10:99167600-99172800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr10:99167600-99172800	Weak transcription	Thymus	Thymus
13	chr10:99167600-99172800	Weak transcription	HUVEC	blood vessel
14	chr10:99167600-99173400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:99167600-99173400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:99167600-99173400	Weak transcription	Esophagus	oesophagus
17	chr10:99167600-99173600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr10:99167600-99173600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:99167600-99174800	Weak transcription	Brain Anterior Caudate	brain
20	chr10:99167600-99177800	Weak transcription	Fetal Intestine Large	intestine
21	chr10:99167600-99178000	Weak transcription	Fetal Muscle Leg	muscle
22	chr10:99167600-99178400	Weak transcription	Right Atrium	heart
23	chr10:99167600-99185200	Weak transcription	Fetal Intestine Small	intestine
24	chr10:99167600-99185200	Weak transcription	Left Ventricle	heart
25	chr10:99167800-99173400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:99167800-99178000	Weak transcription	A549	lung
27	chr10:99168000-99173400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr10:99168800-99178000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr10:99169400-99175200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr10:99169600-99173400	Weak transcription	Primary B cells from cord blood	blood
31	chr10:99170600-99175000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr10:99170600-99175200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr10:99171000-99174800	Enhancers	HepG2	liver
34	chr10:99171200-99173800	Enhancers	K562	blood
35	chr10:99171200-99175200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr10:99171400-99172800	Weak transcription	Osteobl	bone
37	chr10:99171400-99173600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:99171400-99177800	Weak transcription	Fetal Kidney	kidney
39	chr10:99171400-99179400	Weak transcription	Spleen	Spleen
40	chr10:99171400-99185200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr10:99171600-99178000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:99171800-99173600	Weak transcription	Fetal Heart	heart
43	chr10:99171800-99174800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr10:99171800-99175200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:99172200-99173800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr10:99172200-99174200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr10:99172200-99175200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr10:99172200-99175200	Enhancers	HMEC	breast
49	chr10:99172400-99173800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr10:99172400-99174200	Enhancers	GM12878-XiMat	blood

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