Variant report

Variant	rs6490177
Chromosome Location	chr12:118796085-118796086
allele	A/C
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	chr12:118795210..118796886-chr12:118801131..118803860,2	K562	blood:
2	chr12:118749913..118751885-chr12:118794829..118796895,2	K562	blood:
3	chr12:118795944..118799029-chr12:118813367..118816891,5	K562	blood:
4	chr12:118789693..118801109-chr12:118805205..118813455,21	K562	blood:
5	chr12:118792933..118800473-chr12:118805927..118813309,24	K562	blood:
6	chr12:118497374..118499405-chr12:118794577..118796696,2	K562	blood:
7	chr12:118791019..118798938-chr12:118809011..118813946,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000176871	Chromatin interaction
ENSG00000270482	Chromatin interaction
ENSG00000135090	Chromatin interaction
ENSG00000111707	Chromatin interaction

Extended variants
information (count: 160 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs10082823	0.91[EUR][1000 genomes]
rs10507286	0.82[CEU][hapmap]
rs1060964	1.00[CEU][hapmap]
rs10850967	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11068880	0.81[ASN][1000 genomes]
rs11068881	0.81[ASN][1000 genomes]
rs11068888	0.80[ASN][1000 genomes]
rs11068889	0.80[ASN][1000 genomes]
rs11068891	0.91[CEU][hapmap];0.86[ASN][1000 genomes]
rs11068892	0.83[ASN][1000 genomes]
rs11068893	0.83[ASN][1000 genomes]
rs11068898	0.85[ASN][1000 genomes]
rs11068899	0.85[ASN][1000 genomes]
rs11068901	0.85[ASN][1000 genomes]
rs11068904	0.85[ASN][1000 genomes]
rs11068906	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11068908	0.91[CEU][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11068909	0.85[ASN][1000 genomes]
rs11068910	0.83[EUR][1000 genomes]
rs11068914	0.91[ASN][1000 genomes]
rs11068915	0.91[ASN][1000 genomes]
rs11068916	0.92[ASN][1000 genomes]
rs11068917	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068919	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068920	0.96[ASN][1000 genomes]
rs11068922	0.97[ASN][1000 genomes]
rs11068923	0.95[ASN][1000 genomes]
rs11068924	0.94[ASN][1000 genomes]
rs11068926	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11068930	0.89[ASN][1000 genomes]
rs11068933	0.83[ASN][1000 genomes]
rs12227411	0.85[ASN][1000 genomes]
rs12227974	0.85[ASN][1000 genomes]
rs12228425	0.85[ASN][1000 genomes]
rs12229607	0.92[CEU][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12230104	0.89[ASN][1000 genomes]
rs12231358	0.96[ASN][1000 genomes]
rs12231845	0.83[ASN][1000 genomes]
rs12308475	0.82[EUR][1000 genomes]
rs16948193	0.91[CEU][hapmap]
rs16948197	0.91[CEU][hapmap]
rs16948204	0.91[CEU][hapmap]
rs16948230	0.83[CEU][hapmap]
rs16948234	0.91[CEU][hapmap]
rs16948250	1.00[CEU][hapmap]
rs17440315	0.82[CEU][hapmap]
rs17440336	0.82[CEU][hapmap]
rs17440364	0.82[CEU][hapmap]
rs17440433	0.82[CEU][hapmap]
rs17440669	1.00[CEU][hapmap]
rs17440774	1.00[CEU][hapmap]
rs17440823	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs17440893	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17440942	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17440956	1.00[CEU][hapmap]
rs17441033	0.91[CEU][hapmap]
rs17441061	1.00[CEU][hapmap]
rs17441075	0.92[CEU][hapmap]
rs17512142	0.82[CEU][hapmap]
rs17512177	0.81[CEU][hapmap]
rs17512198	0.82[CEU][hapmap]
rs17512219	0.84[CEU][hapmap]
rs17512407	0.92[CEU][hapmap]
rs17512483	1.00[CEU][hapmap]
rs17512525	1.00[CEU][hapmap]
rs17512574	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs17512609	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs17512644	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17512652	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17512763	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17586342	0.82[CEU][hapmap]
rs17586582	0.82[ASN][1000 genomes]
rs17619702	0.81[ASN][1000 genomes]
rs17619805	0.85[ASN][1000 genomes]
rs17619932	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1909617	0.83[EUR][1000 genomes]
rs2036314	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2036489	0.93[EUR][1000 genomes]
rs2055534	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2062519	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2062520	0.94[ASN][1000 genomes]
rs2271007	0.87[ASN][1000 genomes]
rs2280711	0.82[CEU][hapmap]
rs2784	1.00[CEU][hapmap]
rs4442583	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4766899	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4766900	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4767669	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4767670	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4767671	1.00[CEU][hapmap]
rs4767672	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs56133316	0.83[EUR][1000 genomes]
rs56157623	0.83[EUR][1000 genomes]
rs56284927	0.84[EUR][1000 genomes]
rs56324376	0.93[EUR][1000 genomes]
rs59594854	0.93[EUR][1000 genomes]
rs61943365	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61943367	0.83[EUR][1000 genomes]
rs61943368	0.83[EUR][1000 genomes]
rs61943369	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61943370	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61943371	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61943385	0.83[EUR][1000 genomes]
rs61943388	0.83[EUR][1000 genomes]
rs61943389	0.83[EUR][1000 genomes]
rs61943391	0.83[EUR][1000 genomes]
rs61943392	0.83[EUR][1000 genomes]
rs61943393	0.83[EUR][1000 genomes]
rs61943397	0.84[EUR][1000 genomes]
rs61943399	0.83[EUR][1000 genomes]
rs61943400	0.83[EUR][1000 genomes]
rs61943401	0.83[EUR][1000 genomes]
rs61943402	0.83[EUR][1000 genomes]
rs61943403	0.84[EUR][1000 genomes]
rs61943404	0.83[EUR][1000 genomes]
rs61945207	0.82[ASN][1000 genomes]
rs61945219	0.86[ASN][1000 genomes]
rs61946063	0.82[EUR][1000 genomes]
rs6490173	0.92[CEU][hapmap]
rs7132582	0.83[ASN][1000 genomes]
rs7136216	0.82[CEU][hapmap]
rs7136676	1.00[CEU][hapmap]
rs7137055	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7137184	0.83[EUR][1000 genomes]
rs7294498	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7295288	1.00[CEU][hapmap]
rs7296216	0.97[ASN][1000 genomes]
rs7299040	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7302387	0.91[CEU][hapmap]
rs7303417	0.91[CEU][hapmap]
rs7304342	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7305647	1.00[CEU][hapmap]
rs7307393	1.00[CEU][hapmap]
rs7309484	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7309671	1.00[CEU][hapmap]
rs7312555	1.00[CEU][hapmap]
rs7314987	0.91[CEU][hapmap]
rs7315458	0.90[EUR][1000 genomes]
rs73205551	0.84[EUR][1000 genomes]
rs73205576	0.83[EUR][1000 genomes]
rs73205594	0.83[EUR][1000 genomes]
rs73222058	0.84[ASN][1000 genomes]
rs7957828	0.82[EUR][1000 genomes]
rs7961312	0.92[CEU][hapmap]
rs7962185	0.92[CEU][hapmap]
rs7963464	0.86[ASN][1000 genomes]
rs7965350	0.92[CEU][hapmap]
rs7967900	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs7968011	0.83[EUR][1000 genomes]
rs7968371	0.83[EUR][1000 genomes]
rs7974718	0.84[ASN][1000 genomes]
rs884844	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs950288	0.83[EUR][1000 genomes]
rs965524	1.00[CEU][hapmap]
rs9888447	0.85[ASN][1000 genomes]
rs9943819	0.91[CEU][hapmap];0.83[EUR][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	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
3	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
4	nsv899547	chr12:118791441-118896304	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6490177	SUDS3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118791600-118797400	Weak transcription	Gastric	stomach
2	chr12:118792400-118796800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:118793000-118796200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:118793000-118799200	Enhancers	Osteobl	bone
5	chr12:118793200-118796400	Enhancers	Brain Angular Gyrus	brain
6	chr12:118793200-118796400	Enhancers	Fetal Intestine Small	intestine
7	chr12:118793200-118796600	Enhancers	Fetal Intestine Large	intestine
8	chr12:118793200-118797000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr12:118793200-118797800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:118793400-118796200	Enhancers	Brain Substantia Nigra	brain
11	chr12:118793400-118797200	Enhancers	HMEC	breast
12	chr12:118793400-118799200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:118793600-118796800	Enhancers	NHEK	skin
14	chr12:118793600-118797800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr12:118793800-118796400	Enhancers	Colon Smooth Muscle	Colon
16	chr12:118793800-118796600	Enhancers	Adipose Nuclei	Adipose
17	chr12:118793800-118799200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:118794400-118796200	Enhancers	Primary B cells from peripheral blood	blood
19	chr12:118794400-118797800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:118794600-118796400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr12:118794600-118796400	Flanking Active TSS	Dnd41	blood
22	chr12:118794600-118796600	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr12:118794600-118796600	Enhancers	Rectal Smooth Muscle	rectum
24	chr12:118794600-118796600	Enhancers	HSMM	muscle
25	chr12:118794600-118797200	Enhancers	HepG2	liver
26	chr12:118794600-118797800	Active TSS	GM12878-XiMat	blood
27	chr12:118794800-118796200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:118794800-118796600	Enhancers	Liver	Liver
29	chr12:118794800-118807800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:118794800-118808400	Weak transcription	Small Intestine	intestine
31	chr12:118794800-118809000	Weak transcription	Lung	lung
32	chr12:118794800-118809000	Weak transcription	Pancreas	Pancrea
33	chr12:118794800-118809200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:118794800-118809200	Weak transcription	Esophagus	oesophagus
35	chr12:118795000-118796200	Weak transcription	Fetal Stomach	stomach
36	chr12:118795000-118797000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr12:118795000-118797600	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr12:118795200-118796600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:118795200-118796600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr12:118795200-118797200	Active TSS	K562	blood
41	chr12:118795200-118797400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:118795200-118797600	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr12:118795200-118797600	Flanking Active TSS	A549	lung
44	chr12:118795400-118796600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:118795400-118797000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr12:118795400-118797200	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr12:118795400-118797400	Flanking Active TSS	HUVEC	blood vessel
48	chr12:118795400-118797800	Enhancers	NHLF	lung
49	chr12:118795600-118796200	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr12:118795600-118796200	Enhancers	Fetal Lung	lung

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