Variant report

Variant	rs2070561
Chromosome Location	chr21:45657970-45657971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45657604..45660265-chr21:45683962..45685836,2	K562	blood:
2	chr21:45655108..45658029-chr21:45775901..45777424,2	MCF-7	breast:
3	chr21:45620311..45631567-chr21:45651002..45670824,52	MCF-7	breast:
4	chr21:45619816..45631884-chr21:45656529..45663802,30	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232124	Chromatin interaction
ENSG00000232698	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11558819	0.85[EUR][1000 genomes]
rs2070557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2070558	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2070559	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070560	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329718	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56124762	0.92[EUR][1000 genomes]
rs7278257	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
9	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
10	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
11	nsv913901	chr21:45615741-45665330	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv913902	chr21:45615741-45709153	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv470906	chr21:45627976-45661343	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv459295	chr21:45629565-45849864	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
15	nsv587740	chr21:45629565-45849864	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
16	nsv913903	chr21:45630608-45657970	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv913904	chr21:45636881-45700641	Genic enhancers Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	nsv913905	chr21:45640629-45696025	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	nsv913906	chr21:45657970-45818609	Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2070561	FTCD	cis	parietal	SCAN
rs2070561	KRTAP12-1	cis	cerebellum	SCAN
rs2070561	LRRC3	cis	parietal	SCAN
rs2070561	IGSF5	cis	parietal	SCAN
rs2070561	PSMG1	cis	cerebellum	SCAN
rs2070561	KRTAP10-11	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45628600-45659600	Weak transcription	Right Atrium	heart
2	chr21:45632200-45659600	Weak transcription	Fetal Kidney	kidney
3	chr21:45639800-45659400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:45640000-45659000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr21:45643400-45659600	Weak transcription	Hela-S3	cervix
6	chr21:45644800-45659400	Weak transcription	Small Intestine	intestine
7	chr21:45645200-45659200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr21:45646000-45659000	Strong transcription	Fetal Intestine Small	intestine
9	chr21:45646200-45658600	Strong transcription	Liver	Liver
10	chr21:45646200-45658800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr21:45646800-45658400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr21:45646800-45658800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr21:45648400-45658400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr21:45649000-45658600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr21:45652000-45658400	Strong transcription	Gastric	stomach
16	chr21:45653000-45658200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr21:45653000-45658400	Strong transcription	GM12878-XiMat	blood
18	chr21:45653400-45658800	Strong transcription	Primary hematopoietic stem cells	blood
19	chr21:45653600-45658600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr21:45655000-45658000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr21:45655000-45659600	Weak transcription	HUVEC	blood vessel
22	chr21:45655200-45658200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr21:45655200-45659200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr21:45655400-45658200	Weak transcription	NHEK	skin
25	chr21:45655400-45659400	Weak transcription	HMEC	breast
26	chr21:45655600-45658000	Weak transcription	Spleen	Spleen
27	chr21:45655600-45658200	Genic enhancers	Placenta	Placenta
28	chr21:45655800-45659000	Weak transcription	Brain Angular Gyrus	brain
29	chr21:45655800-45659200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr21:45655800-45659200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr21:45656000-45659000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr21:45656000-45659000	Weak transcription	Stomach Mucosa	stomach
33	chr21:45656400-45658400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr21:45656600-45659200	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr21:45656800-45660000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr21:45657000-45658200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr21:45657000-45658400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr21:45657000-45659000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr21:45657000-45659200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr21:45657200-45658200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr21:45657200-45658200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr21:45657200-45658200	Weak transcription	Fetal Intestine Large	intestine
43	chr21:45657200-45658400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr21:45657200-45658400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr21:45657200-45659000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr21:45657200-45659200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr21:45657200-45659200	Weak transcription	Adipose Nuclei	Adipose
48	chr21:45657200-45659200	Weak transcription	Brain Anterior Caudate	brain
49	chr21:45657200-45659200	Weak transcription	Pancreas	Pancrea
50	chr21:45657200-45659600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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