Variant report

Variant	rs674485
Chromosome Location	chr11:65197393-65197394
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:42)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:42 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65196385..65197919-chr20:52494749..52497249,2	MCF-7	breast:
2	chr11:65194680..65197521-chr11:65429706..65431467,2	MCF-7	breast:
3	chr11:65197217..65198018-chr9:131710003..131710975,2	Hela-S3	cervix:
4	chr11:65197029..65197759-chr17:43225330..43226315,2	Hela-S3	cervix:
5	chr11:65196607..65197582-chr11:65236375..65237021,2	MCF-7	breast:
6	chr1:11966803..11968507-chr11:65194382..65198671,3	K562	blood:
7	chr11:65195726..65198598-chr3:73159981..73161523,2	K562	blood:
8	chr11:64618024..64620954-chr11:65196228..65198259,2	K562	blood:
9	chr11:65197032..65197906-chr3:127347967..127348637,2	Hela-S3	cervix:
10	chr11:65195152..65197902-chr11:65335225..65338216,2	K562	blood:
11	chr11:65192842..65197506-chr11:65307614..65311008,4	K562	blood:
12	chr11:65196767..65198789-chr5:137876147..137879117,2	K562	blood:
13	chr11:65195599..65198061-chr16:67902582..67904082,3	K562	blood:
14	chr11:65101646..65104320-chr11:65195923..65197643,2	K562	blood:
15	chr11:65196444..65197434-chr6:20401969..20402967,2	Hela-S3	cervix:
16	chr11:65195117..65198166-chr16:67901081..67904062,3	MCF-7	breast:
17	chr11:65195036..65198002-chr3:176913257..176915574,2	MCF-7	breast:
18	chr11:65195537..65198033-chr12:132622028..132624109,2	K562	blood:
19	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
20	chr11:64937134..64938946-chr11:65196387..65198743,2	K562	blood:
21	chr11:65196303..65197918-chr17:79480504..79482607,2	MCF-7	breast:
22	chr11:65196795..65199135-chr17:58467631..58470553,2	MCF-7	breast:
23	chr1:109234336..109235331-chr11:65197032..65197659,2	Hela-S3	cervix:
24	chr11:65196687..65198439-chr11:65654611..65656258,2	K562	blood:
25	chr11:65195599..65198132-chr16:67902562..67904082,3	K562	blood:
26	chr11:65182317..65198249-chr11:65333937..65346467,45	MCF-7	breast:
27	chr11:65195510..65198202-chr11:65317943..65320475,2	K562	blood:
28	chr11:65195893..65197686-chr19:45926046..45928733,2	MCF-7	breast:
29	chr11:65196354..65198191-chr16:67901061..67902581,2	K562	blood:
30	chr1:28974918..28976832-chr11:65196305..65198800,2	K562	blood:
31	chr11:65195191..65197939-chr6:26027557..26029128,2	K562	blood:
32	chr11:65197155..65199898-chr17:56707507..56709939,2	MCF-7	breast:
33	chr11:65185186..65203592-chr11:65286522..65299399,55	K562	blood:
34	chr11:65196176..65198574-chr17:57930838..57932452,2	MCF-7	breast:
35	chr11:65196773..65198444-chr6:30776938..30778941,2	MCF-7	breast:
36	chr11:65195729..65198013-chr5:81569750..81571966,2	K562	blood:
37	chr11:61559488..61560422-chr11:65197258..65198184,2	Hela-S3	cervix:
38	chr11:65195229..65198024-chr11:65329506..65332495,2	K562	blood:
39	chr11:65197049..65199847-chr11:65380940..65383242,3	K562	blood:
40	chr11:62620935..62622535-chr11:65195409..65198397,2	K562	blood:
41	chr11:65196178..65198624-chr17:59731077..59733987,2	MCF-7	breast:
42	chr11:65041045..65043287-chr11:65194863..65197595,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LTBP3-2	chr11:65193086-65204597	NONHSAT022110

No data

Variant related genes	Relation type
ENSG00000170832	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000142186	Chromatin interaction
ENSG00000114631	Chromatin interaction
ENSG00000270526	Chromatin interaction
ENSG00000141371	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000120705	Chromatin interaction
ENSG00000102898	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000112242	Chromatin interaction
ENSG00000176973	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000173727	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000184009	Chromatin interaction
ENSG00000229848	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000134186	Chromatin interaction
ENSG00000260233	Chromatin interaction
ENSG00000207601	Chromatin interaction
ENSG00000168496	Chromatin interaction
ENSG00000095319	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000134825	Chromatin interaction
ENSG00000012061	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000177565	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1621277	0.83[MEX][hapmap]
rs1626021	0.83[MEX][hapmap]
rs1784859	0.83[MEX][hapmap]
rs2846861	0.83[MEX][hapmap]
rs2904975	0.81[AMR][1000 genomes]
rs512715	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580933	0.81[JPT][hapmap]
rs588298	0.83[MEX][hapmap]
rs595366	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs613316	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs673753	0.81[JPT][hapmap]
rs694243	0.88[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs674485	SCGB2A2	cis	parietal	SCAN
rs674485	STX5	cis	parietal	SCAN
rs674485	NEAT1	cis	Esophagus Mucosa	GTEx
rs674485	NEAT1	cis	Nerve Tibial	GTEx
rs674485	VWCE	cis	parietal	SCAN
rs674485	NEAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs674485	NEAT1	cis	Esophagus Muscularis	GTEx
rs674485	TPCN2	cis	parietal	SCAN
rs674485	CDK2AP2	cis	cerebellum	SCAN
rs674485	NEAT1	cis	Adipose Subcutaneous	GTEx
rs674485	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs674485	NEAT1	cis	Muscle Skeletal	GTEx
rs674485	NEAT1	cis	lung	GTEx
rs674485	MALAT1	cis	parietal	SCAN
rs674485	NEAT1	cis	Thyroid	GTEx
rs674485	NEAT1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65186200-65197400	Active TSS	Psoas Muscle	Psoas
2	chr11:65190400-65199800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:65190400-65200400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
4	chr11:65190600-65206600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:65190800-65201000	Transcr. at gene 5' and 3'	Osteobl	bone
6	chr11:65191000-65197800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:65191000-65206800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:65191200-65198000	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
9	chr11:65191400-65198200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:65192800-65200600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:65193000-65198600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr11:65193200-65198000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr11:65193800-65209800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr11:65194000-65198200	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr11:65194000-65198200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr11:65194000-65198600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr11:65194600-65198000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr11:65194600-65198600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:65194800-65197800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr11:65194800-65198000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:65194800-65198200	Flanking Active TSS	GM12878-XiMat	blood
22	chr11:65194800-65198400	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr11:65194800-65199000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr11:65195000-65197600	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr11:65195000-65197600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:65195000-65198400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr11:65195000-65200000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:65195000-65200400	Enhancers	Primary B cells from peripheral blood	blood
29	chr11:65195200-65197400	Weak transcription	Brain Germinal Matrix	brain
30	chr11:65195200-65197600	Enhancers	Fetal Thymus	thymus
31	chr11:65195200-65197800	Enhancers	Spleen	Spleen
32	chr11:65195200-65198400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr11:65195200-65199200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr11:65195200-65200000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr11:65195400-65197400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:65195400-65197600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr11:65195400-65197800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr11:65195400-65200000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
39	chr11:65195600-65197400	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr11:65195600-65197400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:65195600-65197400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:65195600-65197600	Enhancers	Placenta	Placenta
43	chr11:65195600-65199200	Active TSS	HSMMtube	muscle
44	chr11:65195600-65201600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr11:65195800-65197800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:65195800-65198000	Active TSS	Muscle Satellite Cultured Cells	--
47	chr11:65195800-65201400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr11:65195800-65202000	Weak transcription	Ovary	ovary
49	chr11:65196000-65197400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:65196000-65197400	Weak transcription	Esophagus	oesophagus

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