Variant report

Variant	rs2836660
Chromosome Location	chr21:40123972-40123973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr21:40123876-40124187	HepG2	liver:	n/a	n/a
2	POLR2A	chr21:40123234-40124030	HL-60	blood:	n/a	n/a
3	FOXA1	chr21:40123666-40124230	HepG2	liver:	n/a	n/a
4	FOXA2	chr21:40123709-40124142	HepG2	liver:	n/a	n/a
5	POLR2A	chr21:40123294-40123981	HL-60	blood:	n/a	n/a
6	MAX	chr21:40123570-40124007	NB4	blood:	n/a	n/a
7	FOXA1	chr21:40123681-40124192	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40116268..40119361-chr21:40123830..40126744,3	K562	blood:
2	chr21:40119237..40120879-chr21:40122622..40125319,2	K562	blood:
3	chr21:40123857..40126104-chr21:40126225..40128039,2	MCF-7	breast:
4	chr21:40118598..40121434-chr21:40123073..40125443,2	MCF-7	breast:

No data

Variant related genes	Relation type
LINC00114	TF binding region
ENSG00000223806	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11908743	0.88[YRI][hapmap];0.92[AFR][1000 genomes]
rs2836667	0.81[MKK][hapmap]
rs9982437	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060405	chr21:40095523-40159813	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1057356	chr21:40103881-40147363	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv913739	chr21:40103951-40152372	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv913740	chr21:40103951-40157124	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1066051	chr21:40114130-40147363	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1057627	chr21:40114130-40151977	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1060535	chr21:40114130-40155067	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1063936	chr21:40114130-40159150	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1058591	chr21:40114130-40190594	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv913741	chr21:40116044-40142854	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv459254	chr21:40116044-40152372	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv459255	chr21:40116044-40152372	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv459256	chr21:40116044-40152372	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv459257	chr21:40116044-40152372	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv470900	chr21:40116044-40152372	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv587475	chr21:40116044-40152372	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv459258	chr21:40116044-40157124	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv587476	chr21:40116044-40157124	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv913742	chr21:40116044-40157124	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv516348	chr21:40116044-40161381	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv913743	chr21:40116044-40161381	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv1055623	chr21:40118451-40161072	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2836660	CLIC6	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40102600-40124800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:40115400-40129600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr21:40120200-40124600	Weak transcription	Right Atrium	heart
4	chr21:40120200-40127600	Weak transcription	Spleen	Spleen
5	chr21:40120600-40127400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr21:40120600-40127600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr21:40120800-40124400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr21:40120800-40125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr21:40122000-40125000	Enhancers	Aorta	Aorta
10	chr21:40122600-40128600	Enhancers	Primary hematopoietic stem cells	blood
11	chr21:40122800-40124000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr21:40122800-40125400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr21:40123200-40124200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr21:40123200-40125400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr21:40123400-40124000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr21:40123400-40124200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr21:40123400-40124200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr21:40123400-40124200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr21:40123400-40124200	Enhancers	NH-A	brain
20	chr21:40123400-40124600	Flanking Active TSS	HepG2	liver
21	chr21:40123400-40125200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr21:40123400-40125800	Enhancers	Fetal Intestine Small	intestine
23	chr21:40123600-40124200	Enhancers	Fetal Intestine Large	intestine
24	chr21:40123600-40124200	Enhancers	Fetal Kidney	kidney
25	chr21:40123600-40124400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr21:40123600-40124600	Bivalent Enhancer	Primary B cells from cord blood	blood
27	chr21:40123600-40125200	Bivalent Enhancer	Fetal Stomach	stomach
28	chr21:40123600-40125400	Enhancers	Fetal Muscle Trunk	muscle
29	chr21:40123600-40125400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr21:40123800-40124000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr21:40123800-40124200	Bivalent Enhancer	Osteobl	bone
32	chr21:40123800-40124400	Enhancers	Adipose Nuclei	Adipose
33	chr21:40123800-40125400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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