Variant report

Variant	rs2968005
Chromosome Location	chr5:58318052-58318053
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1078368	0.81[LWK][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap]
rs2968002	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968003	0.89[YRI][hapmap]
rs2968016	0.92[AFR][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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2968005	IL6ST	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
2	chr5:58281800-58321600	Weak transcription	Osteobl	bone
3	chr5:58286200-58330400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:58286200-58330600	Weak transcription	Thymus	Thymus
5	chr5:58288800-58330600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:58296000-58321600	Weak transcription	Aorta	Aorta
7	chr5:58302400-58321600	Weak transcription	Gastric	stomach
8	chr5:58307000-58322000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:58310800-58323400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:58313000-58333400	Weak transcription	Lung	lung
11	chr5:58313200-58325600	Weak transcription	Fetal Lung	lung
12	chr5:58313200-58330200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:58314000-58318600	Strong transcription	Fetal Thymus	thymus
14	chr5:58314200-58318400	Enhancers	Fetal Heart	heart
15	chr5:58314400-58323200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:58314600-58321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:58314800-58318600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr5:58314800-58323000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:58315000-58325800	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:58315200-58318600	Genic enhancers	Primary T cells from cord blood	blood
21	chr5:58315400-58318600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:58316400-58318800	Enhancers	Colon Smooth Muscle	Colon
23	chr5:58316600-58318200	Enhancers	Colonic Mucosa	Colon
24	chr5:58316600-58319200	Enhancers	Hela-S3	cervix
25	chr5:58316800-58318400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr5:58316800-58318400	Enhancers	Rectal Smooth Muscle	rectum
27	chr5:58316800-58318600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:58316800-58318600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr5:58316800-58318600	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr5:58316800-58318600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr5:58316800-58318600	Transcr. at gene 5' and 3'	A549	lung
32	chr5:58317000-58318800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr5:58317200-58318200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:58317200-58318400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr5:58317200-58322800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr5:58317200-58323400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:58317200-58331600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:58317400-58319800	Weak transcription	Fetal Kidney	kidney
39	chr5:58317400-58320600	Weak transcription	Fetal Intestine Large	intestine
40	chr5:58317400-58325200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr5:58317600-58318200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:58317600-58318600	Enhancers	Primary T cells fromperipheralblood	blood
43	chr5:58317600-58318600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr5:58317600-58318600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr5:58317600-58321600	Weak transcription	Right Atrium	heart
46	chr5:58317600-58321600	Weak transcription	HepG2	liver
47	chr5:58317800-58318200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:58317800-58318400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr5:58317800-58318600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:58317800-58318600	Enhancers	Placenta Amnion	Placenta Amnion

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