Variant report

Variant	rs3858490
Chromosome Location	chr11:17540646-17540647
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11024317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs11603262	0.86[YRI][hapmap]
rs2073584	0.81[CEU][hapmap]
rs7119876	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs878208	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv33415	chr11:17532596-17549436	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17516800-17553000	Weak transcription	Stomach Mucosa	stomach
2	chr11:17527600-17549200	Strong transcription	Duodenum Mucosa	Duodenum
3	chr11:17528800-17544000	Weak transcription	Gastric	stomach
4	chr11:17529800-17548600	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr11:17531600-17547200	Strong transcription	Fetal Intestine Large	intestine
6	chr11:17531800-17552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:17532200-17547200	Strong transcription	Fetal Intestine Small	intestine
8	chr11:17533600-17541800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:17535400-17542400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr11:17536200-17542600	Enhancers	Brain Angular Gyrus	brain
11	chr11:17536800-17542400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr11:17537200-17542000	Enhancers	Brain Cingulate Gyrus	brain
13	chr11:17537400-17544800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:17537400-17546800	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:17538000-17542600	Enhancers	Brain Substantia Nigra	brain
16	chr11:17538200-17541200	Weak transcription	Colonic Mucosa	Colon
17	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine
18	chr11:17539400-17540800	Weak transcription	Brain Anterior Caudate	brain
19	chr11:17539400-17541400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr11:17539400-17541600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:17539600-17550000	Weak transcription	Spleen	Spleen
22	chr11:17540000-17542000	Enhancers	Brain Hippocampus Middle	brain
23	chr11:17540200-17541000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:17540400-17540800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:17540400-17541400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr11:17540600-17540800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:17540600-17540800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:17540600-17541200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr11:17540600-17541400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr11:17540600-17541400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr11:17540600-17541600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr11:17540600-17541600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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