Variant report

Variant	rs11068898
Chromosome Location	chr12:118727397-118727398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:118726233..118728965-chr12:118795534..118797544,2	K562	blood:
2	chr12:118727163..118729495-chr12:118743311..118746203,2	K562	blood:

Variant related genes	Relation type
ENSG00000135090	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10850968	0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap]
rs11068853	0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs11068854	0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs11068855	0.82[ASW][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs11068856	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs11068860	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes]
rs11068864	0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068865	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes]
rs11068871	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068872	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11068878	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11068880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068881	0.89[AFR][1000 genomes];0.87[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	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068889	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068891	0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs11068892	0.98[ASN][1000 genomes]
rs11068893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068896	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11068899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068900	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11068901	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068904	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068906	0.95[ASN][1000 genomes]
rs11068908	0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs11068909	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068914	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068915	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068916	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11068917	0.94[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs11068919	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs11068920	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11068922	0.86[ASN][1000 genomes]
rs11068923	0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11068924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11068926	0.82[ASN][1000 genomes]
rs11068930	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068933	0.94[CHB][hapmap];0.94[CHD][hapmap]
rs11068937	0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][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]
rs12227411	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]
rs12227974	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228425	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229607	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs12230104	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12231358	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12231845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16948250	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs17586342	0.88[CHB][hapmap];0.82[CHD][hapmap]
rs17586582	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17619569	0.82[ASW][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17619702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17619805	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17619932	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[ASN][1000 genomes]
rs2036314	0.82[ASN][1000 genomes]
rs2062520	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271007	0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2280711	0.88[CHB][hapmap];0.82[CHD][hapmap]
rs3741444	0.93[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	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136216	0.88[CHB][hapmap];0.82[CHD][hapmap]
rs7296216	0.94[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	0.94[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs9888447	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943792	0.82[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1035497	chr12:118599539-118732144	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541612	chr12:118599539-118732144	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv524938	chr12:118624736-118740675	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
rs11068898	SUDS3	cis	lymphoblastoid	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118652200-118727800	Weak transcription	NHLF	lung
2	chr12:118673400-118737600	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:118673800-118737800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:118676000-118745200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:118677000-118739800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:118683400-118739800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:118692400-118728000	Weak transcription	Adipose Nuclei	Adipose
8	chr12:118693400-118745000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr12:118693600-118728200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:118694600-118739800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:118699200-118737600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:118699800-118727800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:118699800-118733800	Weak transcription	Fetal Stomach	stomach
14	chr12:118699800-118736000	Weak transcription	Fetal Intestine Small	intestine
15	chr12:118700200-118737200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:118700400-118738000	Weak transcription	Fetal Intestine Large	intestine
17	chr12:118702600-118744600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:118704000-118739000	Weak transcription	NHDF-Ad	bronchial
19	chr12:118709800-118737600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:118710800-118738000	Weak transcription	NHEK	skin
21	chr12:118712200-118739000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:118712400-118745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:118712600-118730600	Weak transcription	GM12878-XiMat	blood
24	chr12:118712600-118737400	Weak transcription	Small Intestine	intestine
25	chr12:118712800-118738000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:118714000-118727600	Weak transcription	Esophagus	oesophagus
27	chr12:118715000-118741200	Weak transcription	Thymus	Thymus
28	chr12:118716200-118728000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:118719000-118728000	Weak transcription	Right Ventricle	heart
30	chr12:118719200-118728000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:118719200-118744400	Weak transcription	HSMM	muscle
32	chr12:118719600-118734600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr12:118720600-118734200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:118721200-118730000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr12:118721400-118734800	Weak transcription	Primary B cells from cord blood	blood
37	chr12:118721400-118739800	Weak transcription	Left Ventricle	heart
38	chr12:118721600-118739400	Weak transcription	Psoas Muscle	Psoas
39	chr12:118722400-118737800	Weak transcription	Fetal Lung	lung
40	chr12:118722600-118730400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr12:118722600-118730800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:118722600-118734600	Weak transcription	Dnd41	blood
43	chr12:118722600-118737800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr12:118722600-118739200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:118722600-118745000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:118723800-118728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:118724000-118730000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr12:118724000-118730000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:118724600-118730400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:118725800-118728200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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