Variant report

Variant	rs648601
Chromosome Location	chr11:77586910-77586911
allele	A/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	POLR2A	chr11:77586863-77587353	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:77586083-77587914	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr11:77586705-77587107	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr11:77586164-77588687	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77578952..77581707-chr11:77586888..77589735,2	K562	blood:
2	chr11:77581791..77584975-chr11:77585313..77588016,3	K562	blood:

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

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10899399	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237263	0.91[ASN][1000 genomes]
rs11237280	0.92[EUR][1000 genomes]
rs11237318	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11237338	0.83[GIH][hapmap]
rs11600140	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11606549	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11607032	0.81[ASN][1000 genomes]
rs11607512	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs12279880	0.83[GIH][hapmap]
rs12285765	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286317	0.90[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.91[ASN][1000 genomes]
rs17752006	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17752458	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs1783544	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154972	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305317	0.83[GIH][hapmap]
rs24356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508189	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34130561	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4322421	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4344516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs484363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4945220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56218634	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs588217	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][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]
rs598071	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621456	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs623173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs623907	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs628668	0.90[JPT][hapmap]
rs635195	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636971	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs648896	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs650171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs663674	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs667225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs670090	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs684813	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs687037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs694845	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs695046	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7115801	0.83[GIH][hapmap]
rs7122968	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7123080	1.00[CEU][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72945592	0.91[ASN][1000 genomes]
rs72947668	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72949616	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72949618	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7950873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs7951033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947841	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs648601	INTS4	cis	cerebellum	SCAN
rs648601	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr11:77567600-77589600	Weak transcription	HepG2	liver
7	chr11:77567800-77589400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:77567800-77594800	Weak transcription	Brain Angular Gyrus	brain
9	chr11:77568000-77587000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:77568200-77589400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:77568200-77590400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:77568200-77594600	Weak transcription	Fetal Kidney	kidney
13	chr11:77569000-77597600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:77574600-77593200	Weak transcription	Gastric	stomach
15	chr11:77577400-77588800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:77577400-77589400	Strong transcription	Fetal Muscle Leg	muscle
17	chr11:77577400-77630800	Weak transcription	Fetal Heart	heart
18	chr11:77578200-77589600	Strong transcription	Adipose Nuclei	Adipose
19	chr11:77578400-77589400	Weak transcription	NHDF-Ad	bronchial
20	chr11:77578600-77591400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr11:77578600-77597400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:77578800-77590600	Weak transcription	Hela-S3	cervix
23	chr11:77578800-77601400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:77579000-77593200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:77579200-77625000	Weak transcription	HMEC	breast
26	chr11:77579400-77589400	Weak transcription	NHEK	skin
27	chr11:77579600-77589800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr11:77579800-77589000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:77579800-77589000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:77579800-77597800	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr11:77580000-77597800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:77580200-77597400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr11:77580400-77588400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr11:77580600-77596000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:77580800-77589600	Weak transcription	K562	blood
36	chr11:77580800-77597800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:77581000-77587000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:77581000-77587000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:77581000-77589400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:77581000-77589400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:77581000-77589400	Weak transcription	NH-A	brain
42	chr11:77581000-77589600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr11:77581000-77590000	Weak transcription	Aorta	Aorta
44	chr11:77581000-77597400	Weak transcription	Psoas Muscle	Psoas
45	chr11:77582000-77598000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr11:77582400-77590200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:77582600-77587600	Weak transcription	GM12878-XiMat	blood
48	chr11:77582600-77590000	Strong transcription	Primary B cells from cord blood	blood
49	chr11:77582600-77596000	Strong transcription	Primary T cells from cord blood	blood
50	chr11:77583200-77587200	Weak transcription	Osteobl	bone

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