Variant report

Variant	rs1561876
Chromosome Location	chr11:4113395-4113396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr11:4113265-4113513	K562	blood:	n/a	n/a
2	GABPA	chr11:4113227-4113613	K562	blood:	n/a	n/a
3	SMC3	chr11:4113305-4113581	K562	blood:	n/a	n/a
4	MAZ	chr11:4113246-4113609	K562	blood:	n/a	n/a
5	UBTF	chr11:4113374-4113574	K562	blood:	n/a	n/a
6	UBTF	chr11:4113310-4113609	K562	blood:	n/a	n/a
7	TBP	chr11:4113307-4113637	K562	blood:	n/a	n/a
8	MAFK	chr11:4113194-4113559	K562	blood:	n/a	n/a
9	POLR2A	chr11:4112420-4117868	K562	blood:	n/a	n/a
10	POLR2A	chr11:4113280-4113573	K562	blood:	n/a	n/a
11	POLR2A	chr11:4113095-4113587	HL-60	blood:	n/a	n/a
12	MYC	chr11:4113327-4113603	K562	blood:	n/a	n/a
13	ZNF143	chr11:4113362-4113551	K562	blood:	n/a	n/a
14	POLR2A	chr11:4113237-4113567	K562	blood:	n/a	n/a
15	POLR2A	chr11:4113159-4117790	GM12891	blood:	n/a	n/a
16	ZNF143	chr11:4113359-4113491	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:4102803..4104604-chr11:4111954..4114316,2	K562	blood:
2	chr11:3830403..3832693-chr11:4111742..4114186,3	K562	blood:
3	chr11:4108868..4111240-chr11:4112635..4115203,2	MCF-7	breast:
4	chr11:3859988..3862622-chr11:4113266..4115501,2	K562	blood:
5	chr11:3880710..3882363-chr11:4111617..4114224,2	K562	blood:

No data

Variant related genes	Relation type
RRM1	TF binding region
ENSG00000167323	Chromatin interaction
ENSG00000177105	Chromatin interaction
ENSG00000148985	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1042919	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs1042927	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs10767827	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10767828	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10767851	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs10767853	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10835605	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11030841	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1348310	0.80[CHB][hapmap]
rs1474500	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs1662162	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1735068	0.95[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3794050	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4365044	0.81[CHB][hapmap]
rs4910882	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910883	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910895	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs4910896	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs4910897	0.80[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4910907	0.80[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs4910908	0.80[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs4910909	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs4910910	0.82[JPT][hapmap]
rs4910911	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs4910912	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs6578440	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6578446	0.80[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6578448	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7103860	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7104462	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7933164	0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs7945532	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7946885	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs7951836	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs992980	0.80[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1561876	OR10A4	cis	parietal	SCAN
rs1561876	OR52A1	cis	parietal	SCAN
rs1561876	OR52I2	cis	parietal	SCAN
rs1561876	OR2D2	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4086200-4115200	Weak transcription	NHDF-Ad	bronchial
2	chr11:4087600-4115000	Weak transcription	HSMMtube	muscle
3	chr11:4093800-4115000	Weak transcription	Brain Germinal Matrix	brain
4	chr11:4093800-4115200	Weak transcription	Fetal Kidney	kidney
5	chr11:4094000-4115000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:4094000-4115000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:4094000-4115200	Weak transcription	Brain Substantia Nigra	brain
8	chr11:4098200-4115000	Weak transcription	Hela-S3	cervix
9	chr11:4100200-4115200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:4100600-4115200	Weak transcription	NHLF	lung
11	chr11:4101400-4113600	Strong transcription	Primary B cells from cord blood	blood
12	chr11:4101400-4114000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr11:4101400-4114200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr11:4101600-4113800	Strong transcription	Adipose Nuclei	Adipose
15	chr11:4101800-4113400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:4101800-4114000	Strong transcription	Fetal Stomach	stomach
17	chr11:4102200-4114000	Strong transcription	Spleen	Spleen
18	chr11:4102400-4113400	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:4102400-4115200	Weak transcription	Fetal Brain Male	brain
20	chr11:4103000-4115200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:4103200-4115200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:4103400-4114000	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr11:4104200-4113800	Strong transcription	Fetal Muscle Leg	muscle
24	chr11:4105800-4115200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:4106200-4114200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:4106600-4115400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:4108200-4115000	Weak transcription	NHEK	skin
28	chr11:4108200-4115200	Weak transcription	Brain Hippocampus Middle	brain
29	chr11:4108200-4115200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:4108200-4115400	Weak transcription	Small Intestine	intestine
31	chr11:4108400-4114800	Weak transcription	Pancreas	Pancrea
32	chr11:4108400-4115000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr11:4108400-4115200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:4108400-4115200	Weak transcription	Brain Anterior Caudate	brain
35	chr11:4108600-4115000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:4108600-4115000	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:4108600-4115000	Weak transcription	Psoas Muscle	Psoas
38	chr11:4108800-4115000	Weak transcription	Stomach Mucosa	stomach
39	chr11:4108800-4115200	Weak transcription	Brain Angular Gyrus	brain
40	chr11:4109200-4115000	Weak transcription	HSMM	muscle
41	chr11:4109200-4115000	Weak transcription	Osteobl	bone
42	chr11:4109200-4115200	Weak transcription	HUVEC	blood vessel
43	chr11:4109400-4115000	Weak transcription	HepG2	liver
44	chr11:4109600-4114800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:4109800-4113400	Strong transcription	Esophagus	oesophagus
46	chr11:4110000-4115000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr11:4110000-4115200	Weak transcription	Placenta	Placenta
48	chr11:4110200-4115000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:4110200-4115000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:4110600-4113600	Strong transcription	Rectal Mucosa Donor 31	rectum

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