Variant report

Variant	rs6517612
Chromosome Location	chr21:17118295-17118296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr21:17118246-17118446	K562	blood:	n/a	n/a
2	CUX1	chr21:17118258-17118474	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17101583..17104455-chr21:17117901..17120462,3	MCF-7	breast:

Variant related genes	Relation type
RBPMSLP	TF binding region
ENSG00000155313	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11909953	0.92[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs11910884	0.89[YRI][hapmap]
rs13347185	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17241402	0.92[CHB][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17307156	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1986788	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2026853	0.83[YRI][hapmap]
rs2823464	0.91[CHB][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2823467	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2823469	0.85[AFR][1000 genomes]
rs2823470	0.87[AFR][1000 genomes]
rs2823472	0.83[YRI][hapmap];0.87[AFR][1000 genomes]
rs2823473	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2823477	1.00[CHB][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823479	1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823480	1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823482	0.81[LWK][hapmap];0.91[MEX][hapmap];0.86[YRI][hapmap]
rs2823487	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2823488	1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2823489	0.83[YRI][hapmap]
rs28730511	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55804442	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58134477	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58683309	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60174740	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6517609	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs6517611	0.87[AFR][1000 genomes]
rs6517613	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs6517648	0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs6517652	0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs722887	0.83[AFR][1000 genomes]
rs7277813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7279157	0.82[AFR][1000 genomes]
rs7279170	0.83[AFR][1000 genomes]
rs7283707	0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs8127158	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs8130607	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8134327	1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs926612	0.85[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9305754	0.92[CHB][hapmap]
rs9680115	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9941829	0.83[AFR][1000 genomes]
rs9977019	0.92[CHB][hapmap]
rs9982479	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762093	chr21:16948663-17145770	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1064683	chr21:16954570-17145758	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv459099	chr21:16956866-17145011	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv587076	chr21:16956866-17145011	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1062105	chr21:16956885-17141961	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544380	chr21:16956885-17141961	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1059500	chr21:16957752-17145758	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv1815433	chr21:17106192-17167353	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17104200-17133400	Weak transcription	Colonic Mucosa	Colon
2	chr21:17104600-17123400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr21:17105400-17119400	Weak transcription	Brain Angular Gyrus	brain
4	chr21:17105400-17125200	Weak transcription	Brain Substantia Nigra	brain
5	chr21:17109400-17121000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr21:17112800-17123400	Weak transcription	Brain Hippocampus Middle	brain
7	chr21:17113400-17123600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr21:17113400-17124800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr21:17114200-17121400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr21:17114400-17121400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr21:17114600-17121200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr21:17114600-17123800	Weak transcription	Brain Anterior Caudate	brain
13	chr21:17114800-17119400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr21:17114800-17120800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr21:17114800-17121000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr21:17114800-17121200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr21:17114800-17121200	Weak transcription	Fetal Lung	lung
18	chr21:17114800-17121200	Weak transcription	Hela-S3	cervix
19	chr21:17114800-17121400	Weak transcription	NHLF	lung
20	chr21:17114800-17121800	Weak transcription	Osteobl	bone
21	chr21:17114800-17126600	Weak transcription	Aorta	Aorta
22	chr21:17114800-17126600	Weak transcription	NH-A	brain
23	chr21:17115000-17120200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr21:17115000-17121000	Weak transcription	Fetal Heart	heart
25	chr21:17115000-17121200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr21:17115000-17121600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr21:17115000-17121600	Weak transcription	Stomach Mucosa	stomach
28	chr21:17115000-17122000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr21:17115000-17126600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr21:17115200-17120000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr21:17115200-17120200	Weak transcription	Liver	Liver
32	chr21:17115200-17120400	Weak transcription	Small Intestine	intestine
33	chr21:17115200-17121000	Weak transcription	HUVEC	blood vessel
34	chr21:17115200-17121400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr21:17115200-17122200	Weak transcription	HSMM	muscle
36	chr21:17115200-17130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr21:17115400-17120000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr21:17115400-17122200	Weak transcription	Psoas Muscle	Psoas
39	chr21:17115400-17122200	Weak transcription	Right Atrium	heart
40	chr21:17115400-17123400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr21:17115400-17145400	Weak transcription	Fetal Thymus	thymus
42	chr21:17115600-17118600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr21:17115600-17133400	Weak transcription	Dnd41	blood
44	chr21:17115600-17139400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr21:17115800-17120000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr21:17115800-17120000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr21:17115800-17121000	Weak transcription	Fetal Intestine Large	intestine
48	chr21:17115800-17125600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr21:17116000-17120000	Weak transcription	A549	lung
50	chr21:17116000-17120600	Weak transcription	Monocytes-CD14+_RO01746	blood

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