Variant report

Variant	rs12131200
Chromosome Location	chr1:179941214-179941215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179939017..179942607-chr1:179944050..179947079,4	K562	blood:
2	chr1:179857167..179860041-chr1:179939702..179942440,2	K562	blood:
3	chr1:179939932..179942929-chr1:179944050..179946455,4	K562	blood:
4	chr1:179921069..179927710-chr1:179937007..179944258,10	K562	blood:
5	chr1:179845106..179846951-chr1:179940081..179941620,2	K562	blood:
6	chr1:179923393..179926041-chr1:179940410..179942549,3	MCF-7	breast:
7	chr1:179923469..179925582-chr1:179939367..179942471,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000169905	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1048418	1.00[CHD][hapmap]
rs10494524	0.84[EUR][1000 genomes]
rs10913920	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116940	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12118265	1.00[ASN][1000 genomes]
rs12119130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12121845	0.84[TSI][hapmap]
rs12123201	0.84[EUR][1000 genomes]
rs12123560	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12125245	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125592	1.00[ASN][1000 genomes]
rs12126496	1.00[ASN][1000 genomes]
rs12126967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12127784	1.00[ASN][1000 genomes]
rs12129115	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12130673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130675	0.84[EUR][1000 genomes]
rs12130720	0.83[EUR][1000 genomes]
rs12132694	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12133136	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135751	0.84[EUR][1000 genomes]
rs12136091	1.00[CHB][hapmap]
rs12138429	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12139040	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139323	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12139412	0.84[EUR][1000 genomes]
rs12140622	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141817	0.84[EUR][1000 genomes]
rs12142457	1.00[CHB][hapmap]
rs12144275	0.84[EUR][1000 genomes]
rs12144328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12144346	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144853	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145411	0.84[EUR][1000 genomes]
rs12184265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16855019	0.84[EUR][1000 genomes]
rs16855021	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs16855022	0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs16855025	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs16855048	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs16855049	0.84[EUR][1000 genomes]
rs16855052	0.84[EUR][1000 genomes]
rs16855107	0.84[TSI][hapmap]
rs16855110	0.84[TSI][hapmap]
rs16855125	0.80[CEU][hapmap]
rs16855130	0.84[TSI][hapmap]
rs17299006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371267	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371308	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1801795	1.00[ASN][1000 genomes]
rs3845388	1.00[CHD][hapmap]
rs3856048	0.84[EUR][1000 genomes]
rs3856049	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4301600	1.00[CHD][hapmap]
rs57165548	0.83[EUR][1000 genomes]
rs58463801	0.84[EUR][1000 genomes]
rs61014689	0.84[EUR][1000 genomes]
rs73032352	0.84[EUR][1000 genomes]
rs73039990	0.84[EUR][1000 genomes]
rs73039999	0.84[EUR][1000 genomes]
rs73040001	0.84[EUR][1000 genomes]
rs9701232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701237	0.84[EUR][1000 genomes];1.00[ASN][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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12131200	RALGPS2	cis	parietal	SCAN
rs12131200	CPNE7	trans	cerebellum	SCAN
rs12131200	CEP350	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179924800-179963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:179925200-179946200	Weak transcription	Stomach Mucosa	stomach
3	chr1:179925400-179946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:179926800-179961400	Weak transcription	A549	lung
5	chr1:179927000-179965600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:179934600-179945000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:179936000-179946400	Weak transcription	NHLF	lung
8	chr1:179936200-179946000	Weak transcription	Fetal Lung	lung
9	chr1:179936200-179946000	Weak transcription	HepG2	liver
10	chr1:179936400-179955600	Weak transcription	Dnd41	blood
11	chr1:179936600-179958800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:179937600-179941400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:179937600-179941400	Enhancers	Brain Hippocampus Middle	brain
14	chr1:179937800-179941400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr1:179937800-179941600	Enhancers	Brain Angular Gyrus	brain
16	chr1:179937800-179941600	Enhancers	Brain Anterior Caudate	brain
17	chr1:179937800-179946200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:179938000-179941400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:179938000-179941400	Enhancers	Adipose Nuclei	Adipose
20	chr1:179938000-179983200	Weak transcription	Brain Germinal Matrix	brain
21	chr1:179938400-179941600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:179938400-179943800	Weak transcription	Aorta	Aorta
23	chr1:179938400-179948600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:179938600-179941400	Enhancers	Brain Cingulate Gyrus	brain
25	chr1:179938600-179942200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:179938600-179943200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:179938600-179945400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:179938600-179946000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:179938600-179946000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:179938600-179946000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:179938600-179946000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:179938600-179954600	Weak transcription	Fetal Thymus	thymus
33	chr1:179938600-179956400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:179938600-179956800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:179938600-179956800	Weak transcription	Fetal Intestine Small	intestine
36	chr1:179938600-179956800	Weak transcription	Fetal Stomach	stomach
37	chr1:179938600-179957600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:179938600-179959000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:179938600-179965800	Weak transcription	Esophagus	oesophagus
40	chr1:179938600-179975800	Weak transcription	Thymus	Thymus
41	chr1:179938600-179983200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:179938600-179984600	Weak transcription	Lung	lung
43	chr1:179938800-179942400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr1:179938800-179942400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:179938800-179953400	Weak transcription	Fetal Intestine Large	intestine
46	chr1:179938800-179959800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:179939000-179943400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr1:179939000-179945400	Weak transcription	Osteobl	bone
49	chr1:179939000-179946000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:179939000-179948800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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