Variant report

Variant	rs11181422
Chromosome Location	chr12:42718552-42718553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr12:42717644-42721241	Hela-S3	cervix:	n/a	n/a
2	FOXA2	chr12:42718548-42718970	HepG2	liver:	n/a	n/a
3	FOXA1	chr12:42718508-42719041	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:42718314..42720744-chr12:42735500..42738358,4	K562	blood:
2	chr12:42718161..42719676-chr12:42732826..42735743,2	MCF-7	breast:
3	chr12:42630581..42632543-chr12:42717454..42720310,3	MCF-7	breast:
4	chr12:42536402..42539877-chr12:42717128..42721445,5	MCF-7	breast:
5	chr12:42537125..42540322-chr12:42717377..42722308,7	MCF-7	breast:
6	chr12:42629683..42634871-chr12:42717173..42721669,10	K562	blood:

No data

Variant related genes	Relation type
PPHLN1	TF binding region
ENSG00000015153	Chromatin interaction
ENSG00000151233	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10459290	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs10492388	0.83[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs1051453	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1059360	0.83[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs10785333	0.83[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs10785334	0.83[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs10880259	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs10880260	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10880261	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs10880264	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10880268	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs10880269	0.84[CHB][hapmap]
rs10880283	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880294	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11181364	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11181398	0.80[EUR][1000 genomes]
rs11181399	0.80[EUR][1000 genomes]
rs11181454	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11181465	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181466	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181467	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181483	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181499	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11181501	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11181502	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11181507	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12228205	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12308219	0.80[EUR][1000 genomes]
rs12366848	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12371615	0.83[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12371762	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12423048	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12815283	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12820154	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1551210	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1669886	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1669892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1669893	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1669904	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1669907	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1669910	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1669936	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17551006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1796380	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1796381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1796382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1796384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1796386	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1796388	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1796394	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1839935	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2178753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2406674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406875	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2600908	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2708058	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2708059	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3747557	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3747558	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3810793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4359266	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4768399	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768402	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768411	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768413	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs55702525	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56290913	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61926593	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6582395	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6582398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7133836	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71453350	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7296357	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7305397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7959338	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7965743	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969910	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7970003	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7974654	0.88[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]

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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11181422	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL
rs11181422	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42693600-42719000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:42696200-42718800	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:42697000-42718800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:42699600-42718800	Weak transcription	HUVEC	blood vessel
5	chr12:42701200-42718600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:42701800-42718600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:42701800-42718800	Weak transcription	Brain Angular Gyrus	brain
8	chr12:42701800-42719400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:42702200-42718600	Weak transcription	Brain Substantia Nigra	brain
10	chr12:42702600-42718800	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:42703800-42718800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:42705200-42718600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:42705200-42718600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:42705200-42719000	Weak transcription	HSMMtube	muscle
15	chr12:42705400-42719200	Weak transcription	Fetal Intestine Small	intestine
16	chr12:42705600-42719200	Weak transcription	Psoas Muscle	Psoas
17	chr12:42705600-42719400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:42705600-42719400	Weak transcription	Small Intestine	intestine
19	chr12:42705800-42718600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:42705800-42719400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:42706000-42719400	Weak transcription	Aorta	Aorta
22	chr12:42706000-42719600	Weak transcription	Spleen	Spleen
23	chr12:42707000-42718600	Weak transcription	NHLF	lung
24	chr12:42707200-42718600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:42707600-42718600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:42707600-42718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:42707800-42718600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:42707800-42718600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:42707800-42718600	Weak transcription	HMEC	breast
30	chr12:42707800-42718800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:42707800-42718800	Weak transcription	NH-A	brain
32	chr12:42707800-42719200	Weak transcription	Right Ventricle	heart
33	chr12:42707800-42719400	Weak transcription	Colonic Mucosa	Colon
34	chr12:42709000-42719400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:42709000-42719400	Weak transcription	Gastric	stomach
36	chr12:42709200-42718600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:42709400-42719400	Weak transcription	Esophagus	oesophagus
38	chr12:42709800-42718600	Weak transcription	K562	blood
39	chr12:42710600-42718800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:42710800-42718600	Weak transcription	Brain Anterior Caudate	brain
41	chr12:42711000-42718800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr12:42711000-42719200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:42711200-42718800	Weak transcription	Fetal Brain Male	brain
44	chr12:42711200-42719000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:42711400-42718600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:42711400-42718600	Weak transcription	GM12878-XiMat	blood
47	chr12:42711400-42719200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr12:42711600-42718800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:42712600-42718600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr12:42712600-42719200	Weak transcription	Ovary	ovary

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