Variant report

Variant	rs925531
Chromosome Location	chr12:122153310-122153311
allele	C/T
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:122148985..122154094-chr12:122210649..122217008,11	MCF-7	breast:
2	chr12:122151601..122153571-chr12:122191520..122194326,2	MCF-7	breast:
3	chr12:122148639..122153380-chr12:122238008..122242328,5	MCF-7	breast:
4	chr12:122152731..122155378-chr12:122233490..122235534,2	MCF-7	breast:
5	chr12:122151917..122156679-chr12:122158990..122161990,5	MCF-7	breast:
6	chr12:122147215..122155218-chr12:122185094..122190846,22	MCF-7	breast:
7	chr12:122150615..122153194-chr12:122153260..122155057,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139725	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000139718	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10770182	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs10840612	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11043180	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12320939	0.84[MEX][hapmap]
rs2137434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458402	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2466145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720022	0.84[MEX][hapmap]
rs2720041	0.80[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs2942368	0.84[MEX][hapmap]
rs2942370	0.80[CEU][hapmap]
rs2942379	0.84[MEX][hapmap]
rs2954111	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2954112	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3934658	0.80[MEX][hapmap]
rs7399127	0.80[MEX][hapmap]
rs7967415	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs925531	LRRC43	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122151600-122160800	Weak transcription	Aorta	Aorta
2	chr12:122151600-122186200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:122151800-122154800	Weak transcription	Fetal Kidney	kidney
4	chr12:122151800-122155000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:122151800-122155200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:122151800-122158000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:122151800-122159200	Weak transcription	Esophagus	oesophagus
8	chr12:122151800-122160600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:122152000-122153400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:122152000-122153400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:122152000-122153400	Weak transcription	Thymus	Thymus
12	chr12:122152000-122153600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:122152000-122154600	Weak transcription	HUVEC	blood vessel
14	chr12:122152000-122154800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:122152000-122154800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:122152000-122156600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:122152000-122161200	Weak transcription	Gastric	stomach
18	chr12:122152000-122162600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:122152000-122164000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:122152000-122164000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:122152000-122164600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:122152000-122166400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:122152000-122167400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:122152000-122182200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:122152000-122188000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:122152200-122153400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:122152200-122153400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:122152200-122153400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:122152200-122153400	Weak transcription	Brain Anterior Caudate	brain
30	chr12:122152200-122153400	Enhancers	K562	blood
31	chr12:122152200-122153400	Weak transcription	NHEK	skin
32	chr12:122152200-122153600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:122152200-122154000	Weak transcription	Osteobl	bone
34	chr12:122152200-122154200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:122152200-122154200	Enhancers	Psoas Muscle	Psoas
36	chr12:122152200-122154400	Enhancers	HepG2	liver
37	chr12:122152200-122154600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:122152200-122154600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:122152200-122154800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:122152200-122154800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:122152200-122154800	Weak transcription	Fetal Thymus	thymus
42	chr12:122152200-122154800	Weak transcription	Spleen	Spleen
43	chr12:122152200-122154800	Weak transcription	HSMMtube	muscle
44	chr12:122152200-122154800	Weak transcription	NHDF-Ad	bronchial
45	chr12:122152200-122155000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:122152200-122155000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:122152200-122155000	Weak transcription	NHLF	lung
48	chr12:122152200-122155600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr12:122152200-122157800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:122152200-122157800	Weak transcription	HMEC	breast

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