Variant report

Variant	rs6518323
Chromosome Location	chr21:45226304-45226305
allele	A/G
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:4)
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	chr21:45224876..45229128-chr21:45393312..45396699,5	K562	blood:
2	chr21:45225967..45228845-chr21:45233717..45236389,2	MCF-7	breast:
3	chr21:45225718..45228025-chr21:45244966..45246549,2	MCF-7	breast:
4	chr21:45224931..45227488-chr21:45343356..45345629,2	K562	blood:
5	chr21:45208338..45210438-chr21:45225931..45227738,2	MCF-7	breast:
6	chr21:45226284..45237567-chr21:45281864..45289573,19	K562	blood:
7	chr21:45217580..45220509-chr21:45224777..45226627,2	MCF-7	breast:
8	chr21:45223486..45226473-chr21:45348909..45351794,2	K562	blood:
9	chr21:45224259..45226376-chr21:45393066..45395792,2	K562	blood:
10	chr21:45225840..45228634-chr21:45360679..45363193,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CSTB-1	chr21:45224585-45226469	XLOC_014107
2	lnc-CSTB-1	chr21:45225641-45226469	XLOC_014107
3	lnc-CSTB-1	chr21:45225403-45226469	XLOC_014107
4	lnc-CSTB-1	chr21:45225639-45226469	ENSG00000215458.4

No data

Variant related genes	Relation type
ENSG00000160214	Chromatin interaction
ENSG00000160216	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11701439	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11702496	0.82[EUR][1000 genomes]
rs11702793	0.84[EUR][1000 genomes]
rs11702828	0.88[ASN][1000 genomes]
rs12483706	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13052408	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1573334	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1573335	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1573336	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1964982	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2070539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2186927	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838368	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838372	0.82[CHB][hapmap]
rs2838375	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838384	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838393	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28648592	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35190140	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35196921	0.83[ASN][1000 genomes]
rs3761385	0.87[CHB][hapmap]
rs3819599	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818867	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57786602	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7278524	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8132884	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs880987	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv913876	chr21:45119629-45267193	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2830066	chr21:45133868-45258047	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv913879	chr21:45145286-45237039	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv913880	chr21:45145286-45263920	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv913881	chr21:45145286-45267193	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv470904	chr21:45151045-45258047	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv834107	chr21:45155325-45294546	Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
11	nsv520305	chr21:45175958-45246326	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv913883	chr21:45191139-45252838	Weak transcription Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv913884	chr21:45191139-45255836	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv544469	chr21:45194085-45257959	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv913885	chr21:45206355-45249474	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv587718	chr21:45210932-45252838	Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv1065007	chr21:45212880-45257959	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	nsv544470	chr21:45212880-45257959	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	nsv459292	chr21:45218440-45269841	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
21	nsv587719	chr21:45218440-45269841	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
22	nsv522204	chr21:45220483-45246326	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	nsv913886	chr21:45220483-45267193	Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6518323	LOC284837	cis	cerebellum	SCAN
rs6518323	LOC284837	cis	multi-tissue	Pritchard
rs6518323	LRRC3	cis	parietal	SCAN
rs6518323	CSTB	cis	lymphoblastoid	seeQTL
rs6518323	C21orf2	cis	parietal	SCAN
rs6518323	CSTB	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45211000-45226600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
2	chr21:45211000-45226600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr21:45211000-45229200	Strong transcription	Fetal Intestine Small	intestine
4	chr21:45211000-45230400	Weak transcription	Stomach Mucosa	stomach
5	chr21:45211000-45257200	Weak transcription	Right Atrium	heart
6	chr21:45211200-45226400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr21:45211200-45226800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:45211200-45226800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr21:45211200-45226800	Strong transcription	Esophagus	oesophagus
10	chr21:45211200-45227000	Strong transcription	Primary T cells from cord blood	blood
11	chr21:45211200-45227200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr21:45211200-45227200	Strong transcription	NHEK	skin
13	chr21:45211200-45229400	Strong transcription	Fetal Stomach	stomach
14	chr21:45211200-45230600	Weak transcription	Fetal Brain Male	brain
15	chr21:45211400-45226400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr21:45211400-45226400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr21:45211400-45226600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr21:45211400-45226800	Strong transcription	Brain Anterior Caudate	brain
19	chr21:45211400-45226800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr21:45211400-45226800	Strong transcription	Gastric	stomach
21	chr21:45211400-45227000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr21:45211400-45228200	Strong transcription	Fetal Muscle Leg	muscle
23	chr21:45211600-45226600	Strong transcription	Liver	Liver
24	chr21:45211800-45226400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr21:45211800-45226800	Strong transcription	Lung	lung
26	chr21:45212600-45226800	Strong transcription	Fetal Brain Female	brain
27	chr21:45212600-45228200	Weak transcription	Fetal Kidney	kidney
28	chr21:45212800-45226400	Strong transcription	Dnd41	blood
29	chr21:45212800-45226800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr21:45212800-45227200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr21:45213600-45226800	Strong transcription	Brain Germinal Matrix	brain
32	chr21:45215200-45226600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr21:45215400-45230800	Weak transcription	Small Intestine	intestine
34	chr21:45216200-45226800	Strong transcription	NHLF	lung
35	chr21:45217200-45228600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr21:45217600-45230600	Weak transcription	NHDF-Ad	bronchial
37	chr21:45218400-45230600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr21:45218800-45230600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr21:45219400-45230600	Weak transcription	HUVEC	blood vessel
40	chr21:45219600-45230400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr21:45221800-45230600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr21:45221800-45234200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr21:45222000-45230800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr21:45222400-45230800	Weak transcription	NH-A	brain
45	chr21:45223200-45231000	Weak transcription	HSMM	muscle
46	chr21:45223400-45228200	Weak transcription	HMEC	breast
47	chr21:45223400-45230600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr21:45223400-45230800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr21:45223400-45230800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr21:45223600-45230600	Weak transcription	Brain Angular Gyrus	brain

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