Variant report

Variant	rs13047518
Chromosome Location	chr21:40707307-40707308
allele	A/G
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	chr21:40692981..40695530-chr21:40706938..40709803,5	K562	blood:
4	chr21:40696329..40702419-chr21:40706472..40712889,11	K562	blood:
5	chr21:40624517..40627116-chr21:40705623..40707478,3	MCF-7	breast:
6	21:40702099-40712819..21:40757151-40764378	K562	blood:

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

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1029004	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11088466	0.84[AMR][1000 genomes]
rs11088470	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11701805	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11702505	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11910232	0.82[EUR][1000 genomes]
rs11911087	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12483559	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12627205	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13049907	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1474490	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2056844	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2070865	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2150413	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2150414	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2297256	0.82[AMR][1000 genomes]
rs2836940	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2836942	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2836943	0.82[AMR][1000 genomes]
rs2836945	0.84[AMR][1000 genomes]
rs2836948	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836949	0.80[EUR][1000 genomes]
rs2836952	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836956	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836958	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836959	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836966	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836980	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2836983	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836984	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836985	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34890172	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35769610	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35994303	0.88[EUR][1000 genomes]
rs4816618	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4818018	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4818019	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59916147	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62223011	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62223039	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62223052	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7278297	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7282582	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8127379	0.86[AMR][1000 genomes]
rs8129595	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8130162	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8130320	0.82[AMR][1000 genomes]
rs8133928	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13047518	HMGN1	cis	multi-tissue	Pritchard
rs13047518	PSMG1	cis	Artery Tibial	GTEx
rs13047518	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs13047518	BRWD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 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	chr21:40704600-40708400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr21:40704600-40712600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr21:40704600-40712600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr21:40704600-40712600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr21:40704600-40712600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr21:40704600-40712800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr21:40704600-40712800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr21:40704600-40712800	Weak transcription	Left Ventricle	heart
24	chr21:40704600-40712800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr21:40704600-40713200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr21:40704600-40713200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr21:40704600-40713800	Weak transcription	Ovary	ovary
28	chr21:40704600-40717200	Weak transcription	Right Ventricle	heart
29	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr21:40704800-40708600	Weak transcription	Placenta	Placenta
31	chr21:40704800-40708600	Weak transcription	HepG2	liver
32	chr21:40704800-40712800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr21:40704800-40715200	Weak transcription	Fetal Heart	heart
34	chr21:40705000-40713000	Weak transcription	K562	blood
35	chr21:40705400-40712600	Weak transcription	Brain Cingulate Gyrus	brain

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