Variant report

Variant	rs12293970
Chromosome Location	chr11:104817498-104817499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CASP4-1	chr11:104817351-104817919	NONHSAT023947

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10466650	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10895744	0.81[EUR][1000 genomes]
rs10895752	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11226548	0.83[EUR][1000 genomes]
rs11226549	0.83[EUR][1000 genomes]
rs11226550	0.83[EUR][1000 genomes]
rs11226555	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11226557	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11226562	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11226565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11601896	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11825902	0.81[EUR][1000 genomes]
rs12362084	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12422201	0.83[EUR][1000 genomes]
rs15684	0.83[EUR][1000 genomes]
rs2005513	0.83[EUR][1000 genomes]
rs34436514	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35733341	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4517484	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491011	0.83[EUR][1000 genomes]
rs491945	0.83[EUR][1000 genomes]
rs518553	0.83[EUR][1000 genomes]
rs524060	0.83[EUR][1000 genomes]
rs528641	0.83[EUR][1000 genomes]
rs532705	0.83[EUR][1000 genomes]
rs532738	0.83[EUR][1000 genomes]
rs549691	0.83[EUR][1000 genomes]
rs579156	0.81[EUR][1000 genomes]
rs595395	0.83[EUR][1000 genomes]
rs625046	0.83[EUR][1000 genomes]
rs626771	0.83[EUR][1000 genomes]
rs641046	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs656251	0.83[EUR][1000 genomes]
rs870402	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046098	chr11:104207210-105003661	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv531430	chr11:104380924-105194452	Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv832255	chr11:104674918-104846961	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv898355	chr11:104730322-104897843	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1040784	chr11:104763797-104855878	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv468862	chr11:104774014-105243371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv556218	chr11:104774014-105243371	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv898356	chr11:104779195-104838471	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv3385159	chr11:104786549-105051555	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv1041081	chr11:104797775-104912458	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv1044970	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv541160	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12293970	CASP4	Cis_1M	lymphoblastoid	RTeQTL
rs12293970	CASP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104803400-104819000	Weak transcription	Psoas Muscle	Psoas
2	chr11:104806400-104818200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:104807000-104817800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:104807000-104818200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr11:104807200-104818000	Weak transcription	Left Ventricle	heart
6	chr11:104811400-104818800	Weak transcription	Small Intestine	intestine
7	chr11:104812000-104825200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:104812200-104819000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr11:104812400-104819000	Weak transcription	Aorta	Aorta
10	chr11:104812600-104817800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr11:104812600-104819200	Weak transcription	Gastric	stomach
12	chr11:104812600-104825600	Strong transcription	Placenta	Placenta
13	chr11:104812600-104826800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:104812800-104821600	Weak transcription	Colonic Mucosa	Colon
15	chr11:104812800-104825600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:104812800-104825600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:104812800-104825600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:104812800-104825600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr11:104812800-104826200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr11:104812800-104826600	Strong transcription	Primary hematopoietic stem cells	blood
21	chr11:104812800-104829200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:104812800-104831800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:104813000-104817800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:104813000-104820400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr11:104813000-104825400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:104813000-104825600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:104813000-104825800	Strong transcription	Dnd41	blood
28	chr11:104813200-104817800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr11:104813200-104825400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:104813200-104825400	Strong transcription	Adipose Nuclei	Adipose
31	chr11:104813200-104825600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:104813200-104825800	Strong transcription	Primary T cells from cord blood	blood
33	chr11:104813200-104825800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr11:104813400-104819200	Weak transcription	Thymus	Thymus
35	chr11:104813400-104820200	Weak transcription	HSMMtube	muscle
36	chr11:104813600-104825200	Strong transcription	Ovary	ovary
37	chr11:104813600-104825800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:104813600-104825800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:104813800-104819000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr11:104813800-104826800	Strong transcription	Primary B cells from cord blood	blood
41	chr11:104813800-104837200	Weak transcription	Colon Smooth Muscle	Colon
42	chr11:104814000-104817600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr11:104814000-104822800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:104814000-104838200	Weak transcription	Fetal Kidney	kidney
45	chr11:104814400-104818800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:104814400-104825200	Weak transcription	Fetal Heart	heart
47	chr11:104814400-104825600	Strong transcription	Fetal Muscle Leg	muscle
48	chr11:104814800-104822000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr11:104814800-104825800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:104815000-104819000	Weak transcription	Lung	lung

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