Variant report

Variant	rs8129601
Chromosome Location	chr21:45119104-45119105
allele	C/T
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:0)
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	chr21:45118336..45120442-chr21:45148784..45150627,2	K562	blood:
2	chr21:45118387..45122878-chr21:45135250..45139536,6	K562	blood:
3	chr21:45118243..45120593-chr21:45129634..45132002,2	MCF-7	breast:
4	chr21:45118172..45120404-chr21:45121185..45123941,2	K562	blood:
5	chr21:45118942..45121311-chr21:45147502..45150284,2	K562	blood:
6	chr21:45112710..45116467-chr21:45117620..45123990,9	K562	blood:
7	chr21:45108111..45109755-chr21:45119044..45121389,2	K562	blood:
8	chr21:45118387..45122116-chr21:45137968..45140097,4	K562	blood:
9	chr21:45112896..45115809-chr21:45116596..45119120,4	K562	blood:
10	chr21:45118554..45121566-chr21:45135917..45139666,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160209	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1003280	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs10211901	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1073522	0.81[JPT][hapmap]
rs10854486	0.87[ASN][1000 genomes]
rs11089093	0.98[ASN][1000 genomes]
rs1122873	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs11700909	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11700913	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11702544	0.80[ASN][1000 genomes]
rs11909064	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs12627667	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs13051953	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13053003	0.89[EUR][1000 genomes]
rs1378079	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs1378080	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs141521	0.85[CEU][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs1454648	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1454650	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1454651	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1584917	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1584918	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs1598206	0.89[CEU][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs162343	0.81[CEU][hapmap]
rs162345	0.80[CEU][hapmap]
rs162398	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs2006113	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012989	0.93[EUR][1000 genomes]
rs2070533	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2155722	0.89[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2186924	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236665	0.83[ASN][1000 genomes]
rs2236666	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2236667	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2246602	0.81[JPT][hapmap]
rs2250773	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2251253	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs229357	0.81[JPT][hapmap]
rs2298561	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2298562	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2298563	0.85[EUR][1000 genomes]
rs2329442	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs2329593	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838316	0.80[JPT][hapmap]
rs2838317	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2838318	0.85[CEU][hapmap]
rs2838319	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2838320	1.00[JPT][hapmap]
rs2838321	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2838323	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2838324	0.81[JPT][hapmap]
rs2838325	0.89[CEU][hapmap]
rs2838326	0.89[CEU][hapmap]
rs2838328	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs2838330	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs2838331	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs2838336	0.89[CEU][hapmap]
rs2838337	0.81[JPT][hapmap]
rs2838338	0.81[CEU][hapmap]
rs2838339	0.81[CEU][hapmap]
rs2838340	0.89[CEU][hapmap]
rs2838341	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs2838343	0.89[CEU][hapmap]
rs2838344	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2838345	0.83[ASN][1000 genomes]
rs2838348	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2838350	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838351	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2838353	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3788062	0.81[JPT][hapmap]
rs3819161	0.86[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs389278	0.93[JPT][hapmap]
rs4818850	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs4818858	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4818859	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818860	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818861	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4819270	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs4819283	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4819284	0.85[EUR][1000 genomes]
rs4819285	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819286	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819287	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4819288	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4819289	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819290	0.97[ASN][1000 genomes]
rs4819291	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4819292	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819293	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4819294	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4819295	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4819296	0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6417730	0.88[ASN][1000 genomes]
rs6518301	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs6518302	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs6518309	0.86[JPT][hapmap]
rs6518310	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6518315	0.90[ASN][1000 genomes]
rs7276215	0.81[JPT][hapmap]
rs7276633	0.92[CEU][hapmap]
rs7277539	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs7279958	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs7279959	0.93[JPT][hapmap]
rs7279968	0.88[CEU][hapmap]
rs7282122	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7282405	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7283362	0.82[TSI][hapmap]
rs7283428	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762400	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8131005	0.89[CEU][hapmap]
rs8131027	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8131111	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8133276	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8133523	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs914197	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914198	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306159	0.81[CEU][hapmap]
rs9306160	0.84[CEU][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs9941787	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9976441	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs9977076	0.80[ASN][1000 genomes]
rs9978811	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs9978858	0.80[ASN][1000 genomes]
rs9980185	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs9981291	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs9981790	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs9982727	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9983670	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9983763	0.81[JPT][hapmap]
rs9984002	0.81[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	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv913874	chr21:45041790-45191005	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv531544	chr21:45071371-45202912	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1066728	chr21:45089877-45131723	Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	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
6	nsv1066613	chr21:45108233-45148136	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv3424986	chr21:45118675-45158421	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	esv3329872	chr21:45118725-45158757	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8129601	HSF2BP	cis	Lymphoblastoid	GTEx
rs8129601	HSF2BP	cis	multi-tissue	Pritchard
rs8129601	HSF2BP	cis	lymphoblastoid	seeQTL
rs8129601	DNMT3L	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45080600-45122400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:45080800-45121800	Weak transcription	Fetal Heart	heart
3	chr21:45080800-45122600	Weak transcription	Small Intestine	intestine
4	chr21:45094800-45122000	Weak transcription	Right Atrium	heart
5	chr21:45106800-45120800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr21:45111000-45130600	Weak transcription	HSMM	muscle
7	chr21:45111200-45122800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr21:45111400-45120600	Weak transcription	Stomach Mucosa	stomach
9	chr21:45113000-45122200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr21:45113200-45122600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr21:45113200-45123400	Weak transcription	HSMMtube	muscle
12	chr21:45113800-45121800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr21:45113800-45122400	Weak transcription	Fetal Brain Male	brain
14	chr21:45114000-45122400	Weak transcription	NHDF-Ad	bronchial
15	chr21:45114200-45122600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr21:45114400-45121200	Weak transcription	Brain Angular Gyrus	brain
17	chr21:45114600-45119800	Weak transcription	Brain Substantia Nigra	brain
18	chr21:45114600-45122000	Weak transcription	Esophagus	oesophagus
19	chr21:45114600-45122200	Weak transcription	Psoas Muscle	Psoas
20	chr21:45114600-45123200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr21:45114800-45120600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:45114800-45120800	Weak transcription	GM12878-XiMat	blood
23	chr21:45114800-45122200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr21:45114800-45122200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr21:45114800-45122200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr21:45115000-45119800	Weak transcription	Brain Hippocampus Middle	brain
27	chr21:45115000-45119800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr21:45115000-45120400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr21:45115000-45122200	Weak transcription	Gastric	stomach
30	chr21:45115000-45122800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr21:45115000-45122800	Weak transcription	Fetal Brain Female	brain
32	chr21:45115000-45130800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr21:45115200-45119400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr21:45115200-45122200	Weak transcription	Adipose Nuclei	Adipose
35	chr21:45115400-45119600	Weak transcription	Brain Anterior Caudate	brain
36	chr21:45115400-45120400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr21:45115400-45122400	Weak transcription	Fetal Lung	lung
38	chr21:45115600-45122600	Weak transcription	Osteobl	bone
39	chr21:45115800-45131800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr21:45116000-45122600	Weak transcription	NH-A	brain
41	chr21:45116200-45122000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr21:45116200-45122200	Weak transcription	Placenta	Placenta
43	chr21:45116200-45122400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr21:45116200-45122400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr21:45116200-45122800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr21:45116400-45119200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr21:45116400-45120000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr21:45116400-45121000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr21:45116400-45121800	Weak transcription	Right Ventricle	heart
50	chr21:45116400-45122000	Weak transcription	Brain Germinal Matrix	brain

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