Variant report

Variant	rs608539
Chromosome Location	chr11:77584869-77584870
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr11:77584725-77584915	HepG2	liver:	n/a	n/a
2	MAFK	chr11:77584736-77584934	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77581791..77584975-chr11:77585313..77588016,3	K562	blood:

Variant related genes	Relation type
ENSG00000254459	TF binding region
ENSG00000255449	TF binding region
ENSG00000241782	TF binding region
AAMDC	TF binding region
ENSG00000087884	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs108843	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899396	0.85[ASN][1000 genomes]
rs10899397	0.85[ASN][1000 genomes]
rs10899401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899414	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237264	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237271	0.81[CHB][hapmap]
rs11237279	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11825573	0.81[CHB][hapmap]
rs12294668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12417488	0.81[CHB][hapmap]
rs12418931	0.85[ASN][1000 genomes]
rs12420401	0.81[CHB][hapmap]
rs1544274	0.81[CHB][hapmap]
rs17135807	0.81[CHB][hapmap]
rs1783547	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892869	0.81[CHB][hapmap]
rs1893901	0.81[CHB][hapmap]
rs1986474	0.81[CHB][hapmap]
rs2051484	0.81[CHB][hapmap]
rs2154988	0.81[CHB][hapmap]
rs2186564	0.81[CHB][hapmap]
rs2186573	0.81[CHB][hapmap]
rs2508184	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35711367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3819211	0.81[CHB][hapmap]
rs4531493	0.81[CHB][hapmap]
rs4944176	0.81[CHB][hapmap]
rs4944178	0.81[CHB][hapmap]
rs4945203	0.81[CHB][hapmap]
rs4945204	0.81[CHB][hapmap]
rs4945205	0.81[CHB][hapmap]
rs4945211	0.81[CHB][hapmap]
rs4945219	0.81[CHB][hapmap]
rs570786	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs581807	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs582866	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584732	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585172	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585721	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598933	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600968	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601551	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs603462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608389	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609151	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs611671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611906	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636041	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647235	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649671	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs658398	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs667213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675925	0.83[AFR][1000 genomes]
rs679155	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs679526	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs685474	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694893	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106113	0.81[CHB][hapmap]
rs7116671	0.81[CHB][hapmap]
rs7119471	0.81[CHB][hapmap]
rs7123204	0.81[CHB][hapmap]
rs7127803	0.81[CHB][hapmap]
rs720383	0.81[CHB][hapmap]
rs7925289	0.85[ASN][1000 genomes]
rs7929313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7930066	0.81[CHB][hapmap]
rs7931215	0.81[CHB][hapmap]
rs7936105	0.93[ASN][1000 genomes]
rs7951172	0.81[CHB][hapmap]
rs9667706	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv555453	chr11:77577494-77618441	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv524537	chr11:77583266-77593221	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs608539	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77566000-77592600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr11:77566200-77589000	Weak transcription	NHLF	lung
3	chr11:77566200-77589600	Weak transcription	Esophagus	oesophagus
4	chr11:77566200-77594600	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:77566800-77587800	Weak transcription	A549	lung
6	chr11:77567000-77586600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:77567600-77589600	Weak transcription	HepG2	liver
8	chr11:77567800-77589400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:77567800-77594800	Weak transcription	Brain Angular Gyrus	brain
10	chr11:77568000-77586800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr11:77568000-77587000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:77568200-77589400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:77568200-77590400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:77568200-77594600	Weak transcription	Fetal Kidney	kidney
15	chr11:77569000-77597600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:77574600-77593200	Weak transcription	Gastric	stomach
17	chr11:77576200-77586800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:77577400-77588800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:77577400-77589400	Strong transcription	Fetal Muscle Leg	muscle
20	chr11:77577400-77630800	Weak transcription	Fetal Heart	heart
21	chr11:77578000-77585800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:77578200-77589600	Strong transcription	Adipose Nuclei	Adipose
23	chr11:77578400-77586600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr11:77578400-77589400	Weak transcription	NHDF-Ad	bronchial
25	chr11:77578600-77591400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr11:77578600-77597400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:77578800-77590600	Weak transcription	Hela-S3	cervix
28	chr11:77578800-77601400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:77579000-77593200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr11:77579200-77625000	Weak transcription	HMEC	breast
31	chr11:77579400-77589400	Weak transcription	NHEK	skin
32	chr11:77579600-77589800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr11:77579800-77585200	Strong transcription	Fetal Lung	lung
34	chr11:77579800-77589000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:77579800-77589000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:77579800-77597800	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr11:77580000-77597800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:77580200-77597400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr11:77580400-77588400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:77580600-77596000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:77580800-77589600	Weak transcription	K562	blood
42	chr11:77580800-77597800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:77581000-77586200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:77581000-77587000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr11:77581000-77587000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr11:77581000-77589400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:77581000-77589400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:77581000-77589400	Weak transcription	NH-A	brain
49	chr11:77581000-77589600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr11:77581000-77590000	Weak transcription	Aorta	Aorta

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