Variant report

Variant	rs1963676
Chromosome Location	chr21:40709960-40709961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	21:40553066-40557191..21:40702099-40712819	K562	blood:
2	chr21:40681057..40687929-chr21:40707012..40715318,11	K562	blood:
3	chr21:40696329..40702419-chr21:40706472..40712889,11	K562	blood:
4	21:40702099-40712819..21:40757151-40764378	K562	blood:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000255568	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11088471	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11088472	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11910705	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1882779	0.82[AMR][1000 genomes]
rs1888488	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2005933	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2026267	0.92[AFR][1000 genomes]
rs2037925	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2410123	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2410124	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2735306	0.89[AFR][1000 genomes]
rs2735309	0.92[AFR][1000 genomes]
rs2776307	0.92[AFR][1000 genomes]
rs2776308	0.92[AFR][1000 genomes]
rs2776309	0.92[AFR][1000 genomes]
rs2836981	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836982	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836986	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2836987	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836988	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34240248	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34436313	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35123057	0.92[AFR][1000 genomes]
rs35182074	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4624474	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4818017	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61300849	0.81[ASN][1000 genomes]
rs7279558	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7280326	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7281853	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8127986	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8128827	0.92[AFR][1000 genomes]
rs8130854	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9636957	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs997147	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9978775	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9979483	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9981301	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv587483	chr21:40686327-40718161	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3406100	chr21:40708107-40710655	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1963676	PSMG1	cis	lung	GTEx
rs1963676	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs1963676	PSMG1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40692400-40718400	Weak transcription	Right Atrium	heart
2	chr21:40699200-40712600	Weak transcription	Fetal Muscle Leg	muscle
3	chr21:40704000-40719600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr21:40704200-40712800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr21:40704200-40712800	Weak transcription	A549	lung
6	chr21:40704200-40713200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr21:40704400-40712200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr21:40704400-40712600	Weak transcription	Fetal Intestine Large	intestine
9	chr21:40704400-40712800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr21:40704400-40713000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr21:40704400-40713000	Weak transcription	Fetal Intestine Small	intestine
12	chr21:40704400-40713200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr21:40704400-40713400	Weak transcription	Hela-S3	cervix
14	chr21:40704400-40715000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr21:40704400-40715200	Weak transcription	Spleen	Spleen
16	chr21:40704600-40712600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr21:40704600-40712600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr21:40704600-40712600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr21:40704600-40712600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr21:40704600-40712800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr21:40704600-40712800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr21:40704600-40712800	Weak transcription	Left Ventricle	heart
23	chr21:40704600-40712800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr21:40704600-40713200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr21:40704600-40713200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr21:40704600-40713800	Weak transcription	Ovary	ovary
27	chr21:40704600-40717200	Weak transcription	Right Ventricle	heart
28	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr21:40704800-40712800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr21:40704800-40715200	Weak transcription	Fetal Heart	heart
31	chr21:40705000-40713000	Weak transcription	K562	blood
32	chr21:40705400-40712600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr21:40708600-40712600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr21:40708600-40712800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr21:40708600-40712800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr21:40708800-40712600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr21:40708800-40712600	Weak transcription	Thymus	Thymus
38	chr21:40708800-40712600	Weak transcription	Osteobl	bone
39	chr21:40708800-40712800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr21:40708800-40712800	Weak transcription	Placenta	Placenta
41	chr21:40708800-40713000	Weak transcription	Esophagus	oesophagus
42	chr21:40708800-40713200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr21:40708800-40713400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr21:40708800-40715200	Weak transcription	Gastric	stomach
45	chr21:40709000-40711400	Weak transcription	HepG2	liver
46	chr21:40709000-40713400	Weak transcription	Stomach Mucosa	stomach
47	chr21:40709400-40712800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr21:40709600-40712800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr21:40709600-40713200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr21:40709800-40712600	Weak transcription	Primary T cells fromperipheralblood	blood

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