Variant report

Variant	rs12227411
Chromosome Location	chr12:118750366-118750367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118750220..118752210-chr12:118752581..118754741,2	K562	blood:
2	chr12:118749913..118751885-chr12:118794829..118796895,2	K562	blood:
3	chr12:118746730..118750377-chr12:118808240..118815610,7	K562	blood:

Variant related genes	Relation type
ENSG00000135090	Chromatin interaction
ENSG00000270482	Chromatin interaction
ENSG00000111707	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10850968	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap]
rs11068853	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs11068854	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs11068855	0.88[CHB][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11068856	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs11068860	0.88[CHB][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes]
rs11068864	0.88[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068865	0.88[CHB][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11068871	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068872	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11068878	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11068880	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068881	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068883	0.84[ASN][1000 genomes]
rs11068887	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11068888	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068889	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068891	0.89[ASW][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.95[YRI][hapmap];0.93[ASN][1000 genomes]
rs11068892	0.98[ASN][1000 genomes]
rs11068893	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068896	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11068898	0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068899	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068900	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11068901	0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068906	0.95[ASN][1000 genomes]
rs11068908	0.88[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs11068909	0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068914	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068915	0.94[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068916	0.94[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11068917	0.88[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs11068919	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs11068920	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11068922	0.86[ASN][1000 genomes]
rs11068923	0.88[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11068924	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11068926	0.82[ASN][1000 genomes]
rs11068930	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068933	0.88[CHB][hapmap];0.97[CHD][hapmap]
rs11068937	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11068940	1.00[EUR][1000 genomes]
rs11068941	1.00[EUR][1000 genomes]
rs11068943	1.00[EUR][1000 genomes]
rs11068945	1.00[EUR][1000 genomes]
rs12227974	0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228425	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229607	0.91[ASN][1000 genomes]
rs12230104	1.00[EUR][1000 genomes]
rs12231358	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12231845	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16948250	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs17586342	0.82[CHB][hapmap]
rs17586582	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17619569	0.88[CHB][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17619702	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17619805	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17619932	0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs2036314	0.82[ASN][1000 genomes]
rs2062520	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271007	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2280711	0.82[CHB][hapmap];0.83[YRI][hapmap]
rs3741444	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4442583	0.82[ASN][1000 genomes]
rs61943365	0.89[ASN][1000 genomes]
rs61943369	0.82[ASN][1000 genomes]
rs61943370	0.80[ASN][1000 genomes]
rs61943371	0.80[ASN][1000 genomes]
rs61945207	0.89[ASN][1000 genomes]
rs61945219	0.93[ASN][1000 genomes]
rs6490177	0.85[ASN][1000 genomes]
rs7132582	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136216	0.82[CHB][hapmap]
rs7296216	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73222058	0.91[ASN][1000 genomes]
rs7963464	0.93[ASN][1000 genomes]
rs7974718	0.88[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs9888447	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1038224	chr12:118648415-118791388	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1040061	chr12:118648415-118800437	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1053417	chr12:118688969-118808530	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12227411	SUDS3	cis	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:118732800-118767600	Weak transcription	Primary T cells from cord blood	blood
3	chr12:118738200-118761800	Weak transcription	Fetal Lung	lung
4	chr12:118745400-118768000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:118745600-118750400	Weak transcription	A549	lung
6	chr12:118745600-118751800	Weak transcription	Primary B cells from cord blood	blood
7	chr12:118745800-118766800	Weak transcription	Fetal Intestine Small	intestine
8	chr12:118745800-118767600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:118746000-118750600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:118746000-118783200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:118746200-118766800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:118746200-118785000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:118746400-118754800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:118746600-118751400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:118746600-118752600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:118746600-118756000	Weak transcription	HUVEC	blood vessel
17	chr12:118746600-118766600	Weak transcription	HSMM	muscle
18	chr12:118746800-118751800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:118747000-118751600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:118747000-118754400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:118747000-118759200	Weak transcription	Lung	lung
22	chr12:118747400-118751600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr12:118748000-118756400	Weak transcription	K562	blood
24	chr12:118748000-118772400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr12:118748200-118750400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:118748800-118751000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:118748800-118753200	Enhancers	Primary hematopoietic stem cells	blood
28	chr12:118749200-118751800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:118749200-118754000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr12:118749200-118765800	Weak transcription	Psoas Muscle	Psoas
31	chr12:118749400-118750600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:118749400-118750800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:118749600-118750600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:118749600-118750600	Enhancers	Brain Hippocampus Middle	brain
35	chr12:118749600-118750600	Enhancers	HMEC	breast
36	chr12:118749600-118750600	Enhancers	NHLF	lung
37	chr12:118749600-118750800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:118749600-118750800	Enhancers	Brain Substantia Nigra	brain
39	chr12:118749600-118750800	Enhancers	NHDF-Ad	bronchial
40	chr12:118749600-118750800	Enhancers	Osteobl	bone
41	chr12:118749600-118751000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr12:118749600-118751000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:118749600-118751000	Enhancers	NHEK	skin
44	chr12:118749600-118752800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:118749600-118753800	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr12:118749800-118750400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr12:118749800-118751000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:118750000-118750400	Flanking Active TSS	GM12878-XiMat	blood
49	chr12:118750000-118751000	Enhancers	Liver	Liver
50	chr12:118750200-118750600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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