Variant report

Variant	rs1621277
Chromosome Location	chr11:65221954-65221955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr11:65221885-65223341	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:65221776-65221976	ProgFib	skin:	n/a	n/a
3	POLR2A	chr11:65221313-65224497	U87	brain:	n/a	n/a
4	POLR2A	chr11:65221907-65223320	PANC-1	pancreas:	n/a	n/a
5	CHD1	chr11:65221247-65223345	IMR90	lung:	n/a	n/a
6	POLR2A	chr11:65221644-65223363	U87	brain:	n/a	n/a
7	JUN	chr11:65221883-65223238	K562	blood:	n/a	n/a
8	POLR2A	chr11:65221795-65223245	U87	brain:	n/a	n/a
9	POLR2A	chr11:65221680-65223245	U87	brain:	n/a	n/a
10	POLR2A	chr11:65221721-65224440	PANC-1	pancreas:	n/a	n/a
11	STAT3	chr11:65221914-65222007	MCF10A-Er-Src	breast:	n/a	n/a
12	NR2F2	chr11:65221916-65223235	K562	blood:	n/a	n/a
13	MAX	chr11:65221922-65223226	A549	lung:	n/a	n/a
14	FOSL2	chr11:65221870-65223228	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65122004..65123879-chr11:65220475..65223059,2	K562	blood:
2	chr11:62608095..62609669-chr11:65220631..65223111,2	MCF-7	breast:
3	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173727	TF binding region
ENSG00000245532	Chromatin interaction
ENSG00000173825	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10896000	0.83[AMR][1000 genomes]
rs10896001	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11227204	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1152619	0.86[JPT][hapmap]
rs1616810	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1626021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1784100	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1784101	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1784858	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1784859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1784860	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2105608	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2508711	0.85[ASN][1000 genomes]
rs2508712	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2846861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957268	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2957269	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015965	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3015966	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3016343	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3132743	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3132767	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs512715	0.83[MEX][hapmap]
rs587080	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs587390	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs588298	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs600231	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs602838	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs604676	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605035	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs660588	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs661403	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs674485	0.83[MEX][hapmap]
rs682845	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs694243	0.83[MEX][hapmap]
rs7114809	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7934628	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription 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 miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription 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 miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
15	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
16	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	946 gene(s)	inside rSNPs	diseases
17	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
18	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases
19	nsv541075	chr11:65210592-65331136	Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	620 gene(s)	inside rSNPs	diseases
20	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
21	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' 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	665 gene(s)	inside rSNPs	diseases
22	esv32703	chr11:65213860-65222026	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1621277	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs1621277	SCGB2A2	cis	parietal	SCAN
rs1621277	VWCE	cis	parietal	SCAN
rs1621277	C11orf83	cis	parietal	SCAN
rs1621277	NEAT1	cis	Nerve Tibial	GTEx
rs1621277	STX5	cis	parietal	SCAN
rs1621277	BBS1	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65206600-65222000	Weak transcription	Fetal Kidney	kidney
2	chr11:65210000-65222000	Weak transcription	Brain Angular Gyrus	brain
3	chr11:65210000-65222200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:65210800-65222000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr11:65211400-65222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:65212200-65222000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr11:65212200-65222200	Weak transcription	Liver	Liver
8	chr11:65212400-65222000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:65212400-65222000	Weak transcription	Aorta	Aorta
10	chr11:65212400-65222000	Weak transcription	Fetal Lung	lung
11	chr11:65212600-65222000	Weak transcription	Brain Anterior Caudate	brain
12	chr11:65212800-65222000	Weak transcription	Primary T cells from cord blood	blood
13	chr11:65212800-65222000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:65212800-65222200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr11:65212800-65222400	Weak transcription	Stomach Mucosa	stomach
16	chr11:65213000-65222000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:65213400-65222000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:65213400-65222000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:65213800-65222000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:65213800-65222200	Weak transcription	Gastric	stomach
21	chr11:65213800-65222200	Weak transcription	Pancreas	Pancrea
22	chr11:65214200-65222000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:65214200-65222000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr11:65214200-65222200	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:65214400-65222000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr11:65214400-65222200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:65214400-65222200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:65214600-65222000	Weak transcription	Brain Substantia Nigra	brain
29	chr11:65214600-65222000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:65214600-65222000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:65214800-65222000	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:65217200-65222000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:65219800-65222000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr11:65219800-65222000	Enhancers	Fetal Muscle Leg	muscle
35	chr11:65220000-65222000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:65220000-65222000	Enhancers	NHEK	skin
37	chr11:65220000-65222200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:65220000-65222200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr11:65220000-65222200	Enhancers	HMEC	breast
40	chr11:65220200-65222000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:65220200-65222000	Enhancers	NH-A	brain
42	chr11:65220200-65222200	Enhancers	Esophagus	oesophagus
43	chr11:65220400-65222000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:65220400-65222000	Enhancers	Fetal Muscle Trunk	muscle
45	chr11:65220400-65222200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:65220400-65222200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:65220400-65227000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:65220600-65222000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:65220600-65222000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr11:65220600-65222000	Enhancers	NHDF-Ad	bronchial

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