Variant report

Variant	rs2921057
Chromosome Location	chr8:8318667-8318668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8241927..8245169-chr8:8316549..8319625,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRAGMIN.1-2	chr8:8318630-8318847	ENSG00000254153

Variant related genes	Relation type
ENSG00000182319	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs2921051	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2921053	0.82[AMR][1000 genomes]
rs2921055	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2921056	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2921059	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2921060	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2921061	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2976876	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2976893	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2976902	0.85[AFR][1000 genomes]
rs2976906	0.87[AFR][1000 genomes]
rs2976907	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2976909	0.82[AFR][1000 genomes]
rs2979172	0.82[AMR][1000 genomes]
rs2979179	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2979181	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2979192	0.82[ASN][1000 genomes]
rs2979202	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2980766	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2980767	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2980769	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs876954	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv465448	chr8:8098079-8403142	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' 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	nsv610152	chr8:8098079-8403142	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv610153	chr8:8098079-8454531	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv610154	chr8:8101641-8328101	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1029268	chr8:8130629-8403435	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv539446	chr8:8130629-8403435	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv831227	chr8:8204838-8367160	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
13	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
14	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
15	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv465449	chr8:8262897-8362710	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv610158	chr8:8262897-8362710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv610171	chr8:8290294-8328101	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1025136	chr8:8290818-8326308	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv1034903	chr8:8295208-8324479	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv539454	chr8:8295208-8324479	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv519143	chr8:8296071-8328101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv610172	chr8:8313010-8362710	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv465452	chr8:8313010-8450761	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv610173	chr8:8313010-8450761	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2921057	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs2921057	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs2921057	CTA-398F10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2921057	CTA-398F10.2	cis	Esophagus Mucosa	GTEx
rs2921057	SGK223	cis	Thyroid	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8312200-8321000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr8:8313800-8318800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr8:8313800-8324600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr8:8314000-8319000	Weak transcription	Pancreas	Pancrea
5	chr8:8314000-8320000	Weak transcription	Esophagus	oesophagus
6	chr8:8314000-8320400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:8314000-8325400	Weak transcription	Gastric	stomach
8	chr8:8314200-8318800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr8:8314200-8319200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr8:8315400-8320200	Weak transcription	HSMMtube	muscle
11	chr8:8315400-8322800	Weak transcription	A549	lung
12	chr8:8317000-8318800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:8317200-8320200	Enhancers	Placenta	Placenta
14	chr8:8317600-8320800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr8:8317800-8319000	Enhancers	HepG2	liver
16	chr8:8317800-8324000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:8318200-8319000	Weak transcription	Lung	lung
18	chr8:8318200-8319200	Flanking Active TSS	Dnd41	blood
19	chr8:8318200-8319400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr8:8318200-8320000	Enhancers	Fetal Intestine Large	intestine
21	chr8:8318200-8321800	Enhancers	Duodenum Mucosa	Duodenum
22	chr8:8318400-8320200	Enhancers	Fetal Intestine Small	intestine
23	chr8:8318600-8318800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr8:8318600-8319200	Enhancers	HMEC	breast
25	chr8:8318600-8319400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr8:8318600-8319400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr8:8318600-8319400	Enhancers	Stomach Mucosa	stomach
28	chr8:8318600-8319600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr8:8318600-8319600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr8:8318600-8319600	Weak transcription	Fetal Lung	lung
31	chr8:8318600-8319600	Enhancers	NHEK	skin
32	chr8:8318600-8320000	Enhancers	Thymus	Thymus
33	chr8:8318600-8320600	Enhancers	Fetal Thymus	thymus

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