Variant report

Variant	rs11674894
Chromosome Location	chr2:99818972-99818973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99802213..99804900-chr2:99817713..99819435,2	K562	blood:
2	chr2:99813823..99816682-chr2:99817517..99820204,2	K562	blood:
3	chr2:99813823..99816530-chr2:99816715..99819575,3	K562	blood:

Variant related genes	Relation type
ENSG00000185414	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1044575	0.81[EUR][1000 genomes]
rs10865029	0.88[CEU][hapmap]
rs11123761	0.87[CEU][hapmap]
rs11123765	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11123770	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1133977	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1133978	0.91[EUR][1000 genomes]
rs11677247	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11683107	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11683188	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs11685759	0.86[EUR][1000 genomes]
rs11688004	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs11689265	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs11692336	0.91[EUR][1000 genomes]
rs11692669	0.86[EUR][1000 genomes]
rs11692699	0.87[CEU][hapmap]
rs11695379	0.87[CEU][hapmap]
rs11695751	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11883676	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs11890338	0.81[EUR][1000 genomes]
rs11895749	0.91[EUR][1000 genomes]
rs12613624	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs12619780	0.90[EUR][1000 genomes]
rs12621007	0.87[EUR][1000 genomes]
rs12987548	0.89[EUR][1000 genomes]
rs12991189	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12992218	0.81[EUR][1000 genomes]
rs12992930	0.82[EUR][1000 genomes]
rs12995473	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs12999417	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs13000731	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13008171	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs13008496	0.86[CEU][hapmap]
rs13009147	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs13018891	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs13023501	0.89[EUR][1000 genomes]
rs13023744	0.84[EUR][1000 genomes]
rs13026928	0.83[EUR][1000 genomes]
rs13030961	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs13031919	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13033012	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13035311	0.88[CEU][hapmap]
rs13798	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1453563	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs17759607	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2171359	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2309581	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2516827	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2516828	0.80[EUR][1000 genomes]
rs2516829	0.80[EUR][1000 genomes]
rs2516830	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2516832	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2516833	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2516834	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2516835	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2632260	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2632261	0.80[EUR][1000 genomes]
rs2632277	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2632283	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2632284	0.84[EUR][1000 genomes]
rs2964969	0.82[EUR][1000 genomes]
rs2969379	0.86[EUR][1000 genomes]
rs34252185	0.84[EUR][1000 genomes]
rs34272114	0.91[EUR][1000 genomes]
rs36071868	0.84[EUR][1000 genomes]
rs4340581	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4347885	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4588238	0.87[CEU][hapmap]
rs4850897	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4851187	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs4851188	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs6542864	0.87[CEU][hapmap]
rs6542865	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs6542866	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6542868	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6542869	0.81[EUR][1000 genomes]
rs6542870	0.82[EUR][1000 genomes]
rs6708576	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs6708878	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6717723	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6717729	0.87[CEU][hapmap]
rs6727749	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6733285	0.96[CEU][hapmap]
rs6741772	0.88[CEU][hapmap]
rs6751927	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6753063	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs6753650	0.84[EUR][1000 genomes]
rs6756650	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs6757661	0.82[EUR][1000 genomes]
rs720228	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs720229	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs7349217	0.87[CEU][hapmap]
rs7558004	0.81[EUR][1000 genomes]
rs7572660	0.82[EUR][1000 genomes]
rs7577477	0.88[CEU][hapmap]
rs7604557	0.84[EUR][1000 genomes]
rs7605843	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7608938	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8179690	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs9941561	0.88[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11674894	LIPT1	cis	uninvolved skin	skin_eQTL
rs11674894	LIPT1	cis	lesional skin	skin_eQTL
rs11674894	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs11674894	TSGA10	cis	multi-tissue	Pritchard
rs11674894	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs11674894	TSGA10	cis	Thyroid	GTEx
rs11674894	LIPT1	cis	normal skin	skin_eQTL
rs11674894	TSGA10	cis	lung	GTEx
rs11674894	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs11674894	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs11674894	TSGA10	cis	Lymphoblastoid	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798600-99822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
3	chr2:99798800-99825600	Weak transcription	Fetal Heart	heart
4	chr2:99799200-99824200	Weak transcription	Fetal Brain Male	brain
5	chr2:99803800-99829600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:99806000-99820000	Weak transcription	Colonic Mucosa	Colon
7	chr2:99807000-99832600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:99807600-99825000	Weak transcription	Stomach Mucosa	stomach
9	chr2:99812200-99819000	Weak transcription	NHDF-Ad	bronchial
10	chr2:99814000-99834800	Weak transcription	Gastric	stomach
11	chr2:99814200-99820200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:99814200-99823600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:99814200-99828200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:99814200-99832400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:99814400-99819800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:99814400-99842200	Weak transcription	Ovary	ovary
17	chr2:99814400-99842800	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:99814800-99840600	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:99815000-99823000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:99815000-99829000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:99815000-99834400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:99815000-99836400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:99815000-99840600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:99815000-99840800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:99815000-99841800	Weak transcription	Pancreas	Pancrea
26	chr2:99815000-99842400	Weak transcription	Fetal Lung	lung
27	chr2:99815200-99819400	Weak transcription	Osteobl	bone
28	chr2:99815200-99819600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:99815200-99819600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:99815200-99819800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:99815200-99819800	Weak transcription	NHLF	lung
32	chr2:99815200-99820000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:99815200-99821600	Weak transcription	Fetal Intestine Small	intestine
34	chr2:99815200-99821800	Weak transcription	Placenta	Placenta
35	chr2:99815200-99827400	Weak transcription	HMEC	breast
36	chr2:99815200-99827600	Weak transcription	Brain Germinal Matrix	brain
37	chr2:99815200-99827600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:99815200-99830400	Weak transcription	Brain Anterior Caudate	brain
39	chr2:99815200-99833200	Weak transcription	Lung	lung
40	chr2:99815200-99838400	Weak transcription	Adipose Nuclei	Adipose
41	chr2:99815200-99840600	Weak transcription	Aorta	Aorta
42	chr2:99815200-99841800	Weak transcription	Spleen	Spleen
43	chr2:99815200-99842000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:99815200-99842400	Weak transcription	Brain Substantia Nigra	brain
45	chr2:99815400-99819600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:99815400-99819600	Weak transcription	K562	blood
47	chr2:99815400-99820400	Weak transcription	Right Ventricle	heart
48	chr2:99815400-99820600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:99815400-99821200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:99815400-99821600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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