Variant report

Variant	rs2844720
Chromosome Location	chr6:30475717-30475718
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30463426..30465717-chr6:30474253..30476721,2	MCF-7	breast:
2	chr6:30455599..30458676-chr6:30475156..30481529,8	K562	blood:
3	chr6:30475363..30477327-chr6:30481930..30484322,2	MCF-7	breast:
4	chr6:30475694..30477248-chr6:30510169..30512325,2	MCF-7	breast:
5	chr6:30474018..30476284-chr6:30580992..30583274,2	K562	blood:
6	chr6:30472641..30478529-chr6:30479712..30485715,9	MCF-7	breast:
7	chr6:30470552..30472079-chr6:30475502..30477348,2	MCF-7	breast:
8	chr6:30466122..30468758-chr6:30475477..30477398,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204592	Chromatin interaction
ENSG00000235781	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1058318	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1264432	0.81[EUR][1000 genomes]
rs1264437	0.83[EUR][1000 genomes]
rs1264438	0.83[EUR][1000 genomes]
rs1264439	0.83[EUR][1000 genomes]
rs1264440	0.84[EUR][1000 genomes]
rs1264448	0.81[EUR][1000 genomes]
rs1264456	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1362119	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1468079	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2023608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074503	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2074504	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2074505	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2109477	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2269709	0.86[EUR][1000 genomes]
rs2269710	0.83[EUR][1000 genomes]
rs2429655	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429656	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2508021	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2508022	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2508023	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2508024	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516639	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516641	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2516642	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516643	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516644	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516646	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516647	0.82[EUR][1000 genomes]
rs2516648	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516649	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516653	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516655	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2516656	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516660	0.80[ASN][1000 genomes]
rs2516662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516665	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2524221	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2524223	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2524224	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2524225	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2524226	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2534802	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534803	0.88[EUR][1000 genomes]
rs2534804	0.88[EUR][1000 genomes]
rs2534805	0.86[EUR][1000 genomes]
rs2534806	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2534807	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2534808	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2534809	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2534810	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2534811	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2534812	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2534813	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2534814	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2534815	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534817	0.88[EUR][1000 genomes]
rs2534820	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2534821	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2534823	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534824	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534825	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844713	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844714	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2844715	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844716	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844717	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844721	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2844722	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844725	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3094718	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3095280	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130039	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130041	0.86[EUR][1000 genomes]
rs3130043	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130045	0.86[EUR][1000 genomes]
rs3130240	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3130242	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3130243	0.87[EUR][1000 genomes]
rs3130244	0.88[EUR][1000 genomes]
rs3132609	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3132612	0.84[EUR][1000 genomes]
rs3132613	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3132614	0.89[EUR][1000 genomes]
rs9262070	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9262082	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9262118	0.89[EUR][1000 genomes]
rs975195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996589	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	nsv884076	chr6:30434566-30483919	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
6	nsv884077	chr6:30434900-30512163	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
8	nsv884085	chr6:30462084-30482080	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
10	nsv884088	chr6:30465792-30480434	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv884089	chr6:30465792-30482080	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2844720	HLA-E	cis	multi-tissue	Pritchard
rs2844720	ABT1	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30468600-30476000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:30468800-30483800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:30469000-30476800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:30469200-30477000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:30471200-30475800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr6:30472600-30476600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr6:30472800-30476000	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr6:30472800-30476600	Enhancers	Primary T cells fromperipheralblood	blood
9	chr6:30473200-30476000	Enhancers	Primary T cells from cord blood	blood
10	chr6:30473400-30475800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr6:30473400-30475800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:30473400-30476000	Enhancers	Primary B cells from cord blood	blood
13	chr6:30473600-30475800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr6:30473600-30476200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:30474400-30476400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:30474800-30476400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr6:30475000-30475800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:30475000-30476800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:30475000-30480200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:30475200-30476400	Enhancers	Primary hematopoietic stem cells	blood
21	chr6:30475200-30476400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr6:30475200-30479800	Enhancers	Fetal Thymus	thymus
23	chr6:30475400-30475800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:30475400-30475800	Enhancers	Esophagus	oesophagus
25	chr6:30475400-30476000	Enhancers	Duodenum Mucosa	Duodenum
26	chr6:30475400-30476200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:30475400-30476200	Enhancers	Dnd41	blood
28	chr6:30475400-30476600	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr6:30475400-30476600	Enhancers	Small Intestine	intestine
30	chr6:30475400-30476600	Enhancers	Spleen	Spleen
31	chr6:30475400-30476800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr6:30475400-30476800	Enhancers	Thymus	Thymus
33	chr6:30475400-30477000	Enhancers	Colonic Mucosa	Colon
34	chr6:30475400-30477000	Enhancers	K562	blood
35	chr6:30475400-30477400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:30475400-30477400	Flanking Active TSS	GM12878-XiMat	blood
37	chr6:30475400-30479800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:30475600-30475800	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr6:30475600-30477400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:30475600-30477400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr6:30475600-30478200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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