Variant report

Variant	rs616354
Chromosome Location	chr11:77587973-77587974
allele	C/T
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	chr11:77587934-77588129	K562	blood:	n/a	n/a
2	POLR2A	chr11:77587921-77588205	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:77586164-77588687	K562	blood:	n/a	n/a
4	POLR2A	chr11:77587836-77588260	PFSK-1	brain:	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
AAMDC	TF binding region
ENSG00000254459	TF binding region
ENSG00000254459	Chromatin interaction
ENSG00000255449	Chromatin interaction
ENSG00000241782	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10899415	0.82[CEU][hapmap];0.85[GIH][hapmap]
rs11237265	0.81[EUR][1000 genomes]
rs11601908	0.83[CEU][hapmap]
rs11820337	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12225188	0.81[EUR][1000 genomes]
rs12417115	0.80[ASW][hapmap];0.81[CHD][hapmap];0.82[YRI][hapmap]
rs12418335	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12786047	0.82[CEU][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap]
rs12796422	0.82[CEU][hapmap];0.85[GIH][hapmap]
rs1790238	0.81[CEU][hapmap]
rs1790244	0.82[CEU][hapmap];0.85[GIH][hapmap]
rs1790245	0.81[GIH][hapmap]
rs1790256	0.81[ASW][hapmap];0.82[CEU][hapmap];0.81[GIH][hapmap]
rs1793335	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1793340	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1793344	0.82[CEU][hapmap];0.85[GIH][hapmap]
rs2186562	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2187564	0.81[CEU][hapmap]
rs2276349	0.82[CEU][hapmap]
rs3018167	0.81[ASW][hapmap];0.85[GIH][hapmap]
rs4145700	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs501153	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs529181	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs567814	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs569072	0.80[ASW][hapmap];0.82[YRI][hapmap]
rs618535	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs634477	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs648842	0.92[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs650636	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592751	0.80[CEU][hapmap]
rs665363	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs681411	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs682324	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs687615	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7111625	0.82[EUR][1000 genomes]
rs7115539	0.82[CEU][hapmap]
rs7117813	0.86[ASW][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs7119332	0.86[ASW][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap]
rs7121559	0.81[EUR][1000 genomes]
rs7924567	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7932547	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7941302	0.81[EUR][1000 genomes]
rs7949468	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs616354	OR2AT4	cis	parietal	SCAN
rs616354	INTS4	cis	cerebellum	SCAN
rs616354	KCTD14	cis	cerebellum	SCAN
rs616354	RSF1	cis	cerebellum	SCAN

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	chr11:77567600-77589600	Weak transcription	HepG2	liver
6	chr11:77567800-77589400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:77567800-77594800	Weak transcription	Brain Angular Gyrus	brain
8	chr11:77568200-77589400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:77568200-77590400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:77568200-77594600	Weak transcription	Fetal Kidney	kidney
11	chr11:77569000-77597600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:77574600-77593200	Weak transcription	Gastric	stomach
13	chr11:77577400-77588800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:77577400-77589400	Strong transcription	Fetal Muscle Leg	muscle
15	chr11:77577400-77630800	Weak transcription	Fetal Heart	heart
16	chr11:77578200-77589600	Strong transcription	Adipose Nuclei	Adipose
17	chr11:77578400-77589400	Weak transcription	NHDF-Ad	bronchial
18	chr11:77578600-77591400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:77578600-77597400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:77578800-77590600	Weak transcription	Hela-S3	cervix
21	chr11:77578800-77601400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:77579000-77593200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr11:77579200-77625000	Weak transcription	HMEC	breast
24	chr11:77579400-77589400	Weak transcription	NHEK	skin
25	chr11:77579600-77589800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr11:77579800-77589000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:77579800-77589000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:77579800-77597800	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:77580000-77597800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:77580200-77597400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr11:77580400-77588400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:77580600-77596000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:77580800-77589600	Weak transcription	K562	blood
34	chr11:77580800-77597800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:77581000-77589400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:77581000-77589400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:77581000-77589400	Weak transcription	NH-A	brain
38	chr11:77581000-77589600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:77581000-77590000	Weak transcription	Aorta	Aorta
40	chr11:77581000-77597400	Weak transcription	Psoas Muscle	Psoas
41	chr11:77582000-77598000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr11:77582400-77590200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:77582600-77590000	Strong transcription	Primary B cells from cord blood	blood
44	chr11:77582600-77596000	Strong transcription	Primary T cells from cord blood	blood
45	chr11:77583200-77592400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr11:77583400-77589600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:77583400-77590000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
50	chr11:77583600-77589400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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