Variant report

Variant	rs3791211
Chromosome Location	chr2:99778735-99778736
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99777269..99779242-chr2:99790685..99793650,2	K562	blood:
2	chr2:99770248..99774846-chr2:99775390..99781940,16	K562	blood:
3	chr2:99778714..99780952-chr2:99796631..99798147,2	K562	blood:

Variant related genes	Relation type
ENSG00000185414	Chromatin interaction
ENSG00000273155	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000144182	Chromatin interaction
ENSG00000135951	Chromatin interaction
ENSG00000241962	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10496334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10496335	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123760	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11123767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123768	0.93[EUR][1000 genomes]
rs11526114	0.86[EUR][1000 genomes]
rs12233087	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12620997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1586434	0.86[EUR][1000 genomes]
rs17020569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17022180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17022249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28785294	1.00[EUR][1000 genomes]
rs28794804	0.84[ASN][1000 genomes]
rs34751553	0.81[ASN][1000 genomes]
rs35071324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35458525	0.81[ASN][1000 genomes]
rs3762472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4850895	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs56691336	0.81[ASN][1000 genomes]
rs56926889	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57273701	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57743480	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58595226	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58635701	0.93[EUR][1000 genomes]
rs58745514	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59252741	0.83[ASN][1000 genomes]
rs59506582	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60056452	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60516303	0.84[ASN][1000 genomes]
rs60653099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719145	0.86[EUR][1000 genomes]
rs6746969	0.86[EUR][1000 genomes]
rs6748497	0.86[EUR][1000 genomes]
rs6749198	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7568749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608938	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs9752510	0.86[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	nsv535839	chr2:99742621-99793747	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3791211	LIPT1	cis	multi-tissue	Pritchard
rs3791211	LIPT1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99772200-99795600	Weak transcription	Gastric	stomach
2	chr2:99772400-99781600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:99772400-99782000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:99772400-99782800	Weak transcription	Aorta	Aorta
5	chr2:99772400-99784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:99772400-99784000	Weak transcription	Lung	lung
7	chr2:99772400-99784000	Weak transcription	Spleen	Spleen
8	chr2:99772400-99784800	Weak transcription	Pancreas	Pancrea
9	chr2:99772400-99786200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:99772400-99786200	Weak transcription	Psoas Muscle	Psoas
11	chr2:99772400-99795600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:99772400-99795600	Weak transcription	Small Intestine	intestine
13	chr2:99772400-99796400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:99772400-99796600	Weak transcription	Right Ventricle	heart
15	chr2:99772400-99796800	Weak transcription	Colonic Mucosa	Colon
16	chr2:99772400-99797000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:99772600-99778800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:99772600-99778800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:99772600-99781800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:99772600-99782200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:99772600-99782200	Weak transcription	HUVEC	blood vessel
22	chr2:99772600-99783600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:99772600-99783600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:99772600-99784000	Weak transcription	Thymus	Thymus
25	chr2:99772600-99784200	Weak transcription	HSMMtube	muscle
26	chr2:99772600-99784400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:99772600-99784800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:99772600-99784800	Weak transcription	NH-A	brain
29	chr2:99772600-99786200	Weak transcription	NHLF	lung
30	chr2:99772600-99795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:99772600-99796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:99772600-99796600	Weak transcription	Fetal Kidney	kidney
33	chr2:99772600-99797000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:99772800-99779200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:99772800-99781600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:99772800-99781800	Weak transcription	Osteobl	bone
37	chr2:99772800-99782200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:99772800-99782600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:99772800-99783800	Weak transcription	HMEC	breast
40	chr2:99772800-99784000	Weak transcription	A549	lung
41	chr2:99772800-99786000	Weak transcription	Hela-S3	cervix
42	chr2:99772800-99796400	Weak transcription	Fetal Heart	heart
43	chr2:99773000-99781200	Weak transcription	Fetal Thymus	thymus
44	chr2:99773000-99796400	Weak transcription	Fetal Brain Male	brain
45	chr2:99773200-99779400	Strong transcription	Adipose Nuclei	Adipose
46	chr2:99773200-99779600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:99773200-99779800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:99773200-99790800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:99773400-99779200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr2:99773600-99779800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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