Variant report

Variant	rs2355021
Chromosome Location	chr11:17549409-17549410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:17405170..17406511-chr11:17549006..17550272,4	MCF-7	breast:
2	chr11:17375893..17376701-chr11:17549376..17550298,3	MCF-7	breast:
3	chr11:17404201..17406453-chr11:17548482..17550709,2	K562	blood:
4	chr11:17529263..17531115-chr11:17548910..17550754,2	K562	blood:
5	chr11:17408129..17408789-chr11:17549376..17550314,3	K562	blood:
6	chr11:17251345..17252271-chr11:17549390..17549954,2	K562	blood:
7	chr11:17538690..17542408-chr11:17546927..17550590,3	MCF-7	breast:
8	chr11:17401047..17402845-chr11:17547923..17549749,2	MCF-7	breast:
9	chr11:17408865..17412169-chr11:17547784..17549963,3	K562	blood:
10	chr11:17405141..17406113-chr11:17549390..17550226,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000187486	Chromatin interaction
ENSG00000260196	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12270598	0.85[EUR][1000 genomes]
rs12273896	0.85[EUR][1000 genomes]
rs12275068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16934376	0.85[JPT][hapmap]
rs41282940	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7112757	0.85[EUR][1000 genomes]
rs72870321	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870323	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870330	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs733126	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878545	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs886817	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2355021	SOX6	cis	cerebellum	SCAN

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	chr11:17531800-17552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine
4	chr11:17539600-17550000	Weak transcription	Spleen	Spleen
5	chr11:17540800-17552400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:17541000-17552600	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr11:17541400-17552400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:17541600-17549600	Weak transcription	Brain Anterior Caudate	brain
9	chr11:17541600-17550000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:17541600-17551600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:17541600-17555800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:17542600-17550000	Weak transcription	Brain Substantia Nigra	brain
13	chr11:17544000-17549800	Strong transcription	Colonic Mucosa	Colon
14	chr11:17545400-17553000	Weak transcription	Gastric	stomach
15	chr11:17545800-17550000	Weak transcription	Right Atrium	heart
16	chr11:17546800-17550000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:17547200-17550400	Genic enhancers	Fetal Intestine Large	intestine
18	chr11:17547200-17563200	Genic enhancers	Fetal Intestine Small	intestine
19	chr11:17548000-17550000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:17548000-17550200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr11:17548400-17549600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:17549000-17550400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr11:17549000-17553400	Enhancers	Brain Cingulate Gyrus	brain
24	chr11:17549200-17550800	Enhancers	Brain Germinal Matrix	brain
25	chr11:17549200-17551400	Enhancers	HSMMtube	muscle
26	chr11:17549400-17549600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:17549400-17549600	Bivalent Enhancer	Fetal Stomach	stomach
28	chr11:17549400-17549800	Enhancers	Brain Angular Gyrus	brain
29	chr11:17549400-17550000	Enhancers	Fetal Muscle Leg	muscle
30	chr11:17549400-17550400	Enhancers	Duodenum Mucosa	Duodenum
31	chr11:17549400-17551000	Enhancers	Brain Hippocampus Middle	brain
32	chr11:17549400-17552600	Strong transcription	Rectal Mucosa Donor 29	rectum

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