Variant report

Variant	rs925530
Chromosome Location	chr12:122163276-122163277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122163003..122165142-chr12:122169048..122171086,2	K562	blood:
2	chr12:122156937..122159607-chr12:122159966..122163609,5	K562	blood:
3	chr12:122162572..122165031-chr12:122171808..122174771,2	K562	blood:
4	chr12:122156607..122159627-chr12:122162915..122168187,5	MCF-7	breast:
5	chr12:122138252..122140524-chr12:122161375..122164016,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11043184	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2458404	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2669172	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720027	0.84[GIH][hapmap]
rs2720034	0.86[GIH][hapmap]
rs2720036	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2942375	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2942376	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2942377	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2942378	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs884885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804982	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs925530	LRRC43	cis	cerebellum	SCAN
rs925530	TMEM120B	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122151600-122186200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:122152000-122164000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:122152000-122164000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:122152000-122164600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr12:122152000-122166400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:122152000-122167400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:122152000-122182200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:122152000-122188000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:122152200-122165000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:122152200-122166600	Weak transcription	Ovary	ovary
11	chr12:122152200-122181600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:122152200-122181800	Weak transcription	Right Ventricle	heart
13	chr12:122152200-122186400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:122152200-122188000	Weak transcription	Brain Germinal Matrix	brain
15	chr12:122152200-122188000	Weak transcription	Dnd41	blood
16	chr12:122152200-122191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:122152200-122191600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:122152200-122200200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:122152400-122171600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:122152400-122188000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:122152800-122169200	Weak transcription	Fetal Brain Female	brain
22	chr12:122152800-122186200	Weak transcription	Pancreas	Pancrea
23	chr12:122153600-122166400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:122154000-122182200	Weak transcription	Primary T cells from cord blood	blood
25	chr12:122154200-122165200	Weak transcription	Fetal Intestine Large	intestine
26	chr12:122154200-122200400	Weak transcription	Psoas Muscle	Psoas
27	chr12:122155000-122165200	Weak transcription	HepG2	liver
28	chr12:122155200-122167000	Weak transcription	Lung	lung
29	chr12:122155200-122170000	Weak transcription	Adipose Nuclei	Adipose
30	chr12:122155200-122181600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:122155200-122182400	Weak transcription	NHEK	skin
32	chr12:122155200-122186400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:122155400-122166400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr12:122155400-122166600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:122155400-122169400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:122155400-122178600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:122155600-122186200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:122157000-122174800	Weak transcription	Hela-S3	cervix
39	chr12:122157200-122179600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:122157200-122182400	Weak transcription	GM12878-XiMat	blood
41	chr12:122158200-122171800	Weak transcription	K562	blood
42	chr12:122158800-122163600	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:122158800-122171800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:122158800-122175000	Weak transcription	Osteobl	bone
45	chr12:122158800-122186200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:122158800-122186200	Weak transcription	NHDF-Ad	bronchial
47	chr12:122158800-122186400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:122159000-122186200	Weak transcription	NH-A	brain
49	chr12:122159200-122168400	Weak transcription	Placenta	Placenta
50	chr12:122159200-122170200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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