Variant report

Variant	rs7949293
Chromosome Location	chr11:104830109-104830110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:104829974-104830113	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CASP4	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11606407	1.00[CEU][hapmap];1.00[CHB][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]
rs12417050	1.00[CHB][hapmap]
rs12417470	1.00[CHB][hapmap]
rs12420557	1.00[CHB][hapmap]
rs12420601	1.00[CHB][hapmap]
rs12797298	1.00[CHB][hapmap]
rs12800151	1.00[CHB][hapmap]
rs12801987	1.00[CHB][hapmap]
rs1503391	1.00[CHB][hapmap]
rs1699089	1.00[CHB][hapmap]
rs17103597	1.00[CHB][hapmap]
rs17103670	1.00[CHB][hapmap]
rs17376473	1.00[CHB][hapmap]
rs17446518	1.00[CHB][hapmap]
rs2047841	1.00[CHB][hapmap]
rs2155817	1.00[CHB][hapmap]
rs3181184	1.00[CHB][hapmap]
rs3181327	1.00[CHB][hapmap]
rs3181328	1.00[CHB][hapmap]
rs3181330	1.00[CHB][hapmap]
rs3181334	1.00[CHB][hapmap]
rs34071659	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs475266	1.00[CHB][hapmap]
rs4755080	1.00[CHB][hapmap]
rs481736	1.00[CHB][hapmap]
rs481926	1.00[CHB][hapmap]
rs483345	1.00[CHB][hapmap]
rs484626	1.00[CHB][hapmap]
rs488992	1.00[CHB][hapmap]
rs489715	1.00[CHB][hapmap]
rs490565	1.00[CHB][hapmap]
rs492366	1.00[CHB][hapmap]
rs501626	1.00[CHB][hapmap]
rs504054	1.00[CHB][hapmap]
rs505901	1.00[CHB][hapmap]
rs507438	1.00[CHB][hapmap]
rs507509	1.00[CHB][hapmap]
rs516286	1.00[CHB][hapmap]
rs518878	1.00[CHB][hapmap]
rs526167	1.00[CHB][hapmap]
rs528076	1.00[CHB][hapmap]
rs530009	1.00[CHB][hapmap]
rs534811	1.00[CHB][hapmap]
rs538943	1.00[CHB][hapmap]
rs539595	1.00[CHB][hapmap]
rs542571	1.00[CHB][hapmap]
rs546449	1.00[CHB][hapmap]
rs554344	1.00[CHB][hapmap]
rs556205	1.00[CHB][hapmap]
rs557905	1.00[CHB][hapmap]
rs56014702	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56026330	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56126979	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56184015	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56390038	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568910	1.00[CHB][hapmap]
rs571593	1.00[CHB][hapmap]
rs572031	1.00[CHB][hapmap]
rs572687	1.00[CHB][hapmap]
rs580253	1.00[CHB][hapmap]
rs692897	1.00[CHB][hapmap]
rs692914	1.00[CHB][hapmap]
rs7123277	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928549	1.00[CHB][hapmap]

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
rs7949293	CASP12	cis	cerebellum	SCAN
rs7949293	PDGFD	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104812800-104831800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:104813800-104837200	Weak transcription	Colon Smooth Muscle	Colon
3	chr11:104814000-104838200	Weak transcription	Fetal Kidney	kidney
4	chr11:104817800-104837000	Weak transcription	Right Ventricle	heart
5	chr11:104821200-104836000	Weak transcription	Gastric	stomach
6	chr11:104821800-104831800	Weak transcription	Fetal Stomach	stomach
7	chr11:104821800-104832000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:104821800-104834400	Weak transcription	Thymus	Thymus
9	chr11:104821800-104836600	Weak transcription	Aorta	Aorta
10	chr11:104821800-104837400	Weak transcription	HSMMtube	muscle
11	chr11:104822000-104834200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr11:104822000-104836800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr11:104822200-104831600	Weak transcription	Lung	lung
14	chr11:104822200-104832000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr11:104824200-104832000	Weak transcription	Spleen	Spleen
16	chr11:104824400-104836000	Weak transcription	Psoas Muscle	Psoas
17	chr11:104825000-104831800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:104825200-104831200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:104825200-104831800	Weak transcription	Ovary	ovary
20	chr11:104825200-104832200	Weak transcription	Osteobl	bone
21	chr11:104825200-104834400	Weak transcription	Fetal Lung	lung
22	chr11:104825400-104831600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:104825400-104832800	Weak transcription	Adipose Nuclei	Adipose
24	chr11:104825400-104836400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr11:104825400-104836600	Weak transcription	Left Ventricle	heart
26	chr11:104825400-104836800	Weak transcription	Esophagus	oesophagus
27	chr11:104825400-104837400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:104825400-104838200	Weak transcription	HSMM	muscle
29	chr11:104825600-104830600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:104825600-104831000	Weak transcription	Placenta	Placenta
31	chr11:104825600-104831400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:104825600-104831600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:104825600-104831800	Weak transcription	Fetal Intestine Large	intestine
34	chr11:104825600-104832000	Weak transcription	Fetal Muscle Leg	muscle
35	chr11:104825600-104834200	Weak transcription	Fetal Thymus	thymus
36	chr11:104825600-104835800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr11:104825600-104836800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:104825800-104831800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:104825800-104832000	Weak transcription	Primary T cells from cord blood	blood
40	chr11:104825800-104832000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr11:104825800-104832000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr11:104825800-104835800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:104825800-104836600	Weak transcription	HUVEC	blood vessel
44	chr11:104826000-104831800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:104826000-104832200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr11:104826200-104831200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr11:104826400-104832000	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr11:104826400-104832000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr11:104827000-104831600	Weak transcription	NHLF	lung
50	chr11:104827000-104831800	Weak transcription	Monocytes-CD14+_RO01746	blood

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