Variant report

Variant	rs17241416
Chromosome Location	chr21:17120391-17120392
allele	G/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	STAT3	chr21:17120328-17120503	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17118340..17121294-chr21:17222829..17224563,2	MCF-7	breast:
2	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: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10482875	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10482876	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11910884	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs1543299	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17241395	0.85[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs17241409	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17241423	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17241430	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17241444	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17241460	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17241481	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17275511	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17307120	0.83[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17307170	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17307176	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17307190	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17307197	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17307204	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2026853	1.00[CEU][hapmap]
rs2205585	0.81[EUR][1000 genomes]
rs2205588	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2223176	0.81[EUR][1000 genomes]
rs2242676	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2242680	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2242681	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2245574	0.91[CEU][hapmap]
rs2404000	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2404001	0.83[CEU][hapmap]
rs2823455	0.91[CEU][hapmap]
rs2823457	0.85[CHB][hapmap]
rs2823462	0.83[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823463	0.83[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2823471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823472	0.91[CEU][hapmap]
rs2823478	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2823481	0.85[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2823483	0.94[ASN][1000 genomes]
rs2823484	0.85[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2823489	0.91[CEU][hapmap]
rs2823491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823493	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2823495	0.81[EUR][1000 genomes]
rs2823496	0.81[EUR][1000 genomes]
rs2823498	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2823499	1.00[CEU][hapmap]
rs2823500	1.00[CEU][hapmap]
rs2823504	0.91[CEU][hapmap]
rs28627435	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3787577	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4580465	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55806628	0.82[AMR][1000 genomes]
rs56299770	0.88[EUR][1000 genomes]
rs56333224	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56410772	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56666611	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57733106	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59084861	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59420372	0.90[AMR][1000 genomes]
rs60191002	0.88[EUR][1000 genomes]
rs60529604	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517609	0.91[CEU][hapmap]
rs6517613	0.91[CEU][hapmap]
rs6517648	1.00[CEU][hapmap]
rs6517652	1.00[CEU][hapmap]
rs7277807	0.83[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7278428	0.83[CEU][hapmap];0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs7281511	1.00[CEU][hapmap]
rs7282314	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7283707	1.00[CEU][hapmap]
rs7283764	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs73181987	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73346769	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73355479	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73357260	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73892510	0.87[ASN][1000 genomes]
rs8127158	0.91[CEU][hapmap]
rs8128073	0.82[EUR][1000 genomes]
rs8133079	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8134327	0.91[CEU][hapmap]
rs9981766	0.81[EUR][1000 genomes]
rs9983542	0.85[JPT][hapmap]

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:99 , 50 per page) page: 1 2

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	chr21:17105400-17125200	Weak transcription	Brain Substantia Nigra	brain
4	chr21:17109400-17121000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr21:17112800-17123400	Weak transcription	Brain Hippocampus Middle	brain
6	chr21:17113400-17123600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr21:17113400-17124800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr21:17114200-17121400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr21:17114400-17121400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr21:17114600-17121200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr21:17114600-17123800	Weak transcription	Brain Anterior Caudate	brain
12	chr21:17114800-17120800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr21:17114800-17121000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr21:17114800-17121200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr21:17114800-17121200	Weak transcription	Fetal Lung	lung
16	chr21:17114800-17121200	Weak transcription	Hela-S3	cervix
17	chr21:17114800-17121400	Weak transcription	NHLF	lung
18	chr21:17114800-17121800	Weak transcription	Osteobl	bone
19	chr21:17114800-17126600	Weak transcription	Aorta	Aorta
20	chr21:17114800-17126600	Weak transcription	NH-A	brain
21	chr21:17115000-17121000	Weak transcription	Fetal Heart	heart
22	chr21:17115000-17121200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr21:17115000-17121600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr21:17115000-17121600	Weak transcription	Stomach Mucosa	stomach
25	chr21:17115000-17122000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr21:17115000-17126600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr21:17115200-17120400	Weak transcription	Small Intestine	intestine
28	chr21:17115200-17121000	Weak transcription	HUVEC	blood vessel
29	chr21:17115200-17121400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr21:17115200-17122200	Weak transcription	HSMM	muscle
31	chr21:17115200-17130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr21:17115400-17122200	Weak transcription	Psoas Muscle	Psoas
33	chr21:17115400-17122200	Weak transcription	Right Atrium	heart
34	chr21:17115400-17123400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr21:17115400-17145400	Weak transcription	Fetal Thymus	thymus
36	chr21:17115600-17133400	Weak transcription	Dnd41	blood
37	chr21:17115600-17139400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr21:17115800-17121000	Weak transcription	Fetal Intestine Large	intestine
39	chr21:17115800-17125600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr21:17116000-17120600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr21:17116000-17125400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr21:17116200-17121800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr21:17116200-17124800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr21:17116200-17139400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr21:17116400-17120400	Weak transcription	Spleen	Spleen
46	chr21:17116400-17120600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr21:17116400-17121000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr21:17116400-17121000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr21:17116400-17121800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr21:17116400-17122000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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