Variant report

Variant	rs1465952
Chromosome Location	chr11:4114539-4114540
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	chr11:4113987-4114609	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:4112420-4117868	K562	blood:	n/a	n/a
3	GATA3	chr11:4114415-4114540	SH-SY5Y	brain:	n/a	n/a
4	IRF1	chr11:4114442-4114584	K562	blood:	n/a	chr11:4114521-4114528 chr11:4114514-4114527 chr11:4114513-4114527 chr11:4114516-4114527 chr11:4114514-4114528 chr11:4114512-4114526 chr11:4114516-4114530 chr11:4114515-4114532 chr11:4114514-4114527 chr11:4114514-4114527 chr11:4114516-4114526 chr11:4114513-4114530
5	POLR2A	chr11:4113159-4117790	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:4114277..4116935-chr11:4123036..4125551,3	K562	blood:
2	chr11:4108868..4111240-chr11:4112635..4115203,2	MCF-7	breast:
3	chr11:4109002..4112620-chr11:4113600..4116906,4	MCF-7	breast:
4	chr11:3859988..3862622-chr11:4113266..4115501,2	K562	blood:

Variant related genes	Relation type
RRM1	TF binding region
ENSG00000167323	Chromatin interaction
ENSG00000167325	Chromatin interaction
ENSG00000177105	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10742194	0.86[YRI][hapmap]
rs10742229	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10742249	0.82[JPT][hapmap]
rs10767827	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs11030814	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11602757	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1442725	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1662163	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1735053	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2289570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2412341	0.86[CEU][hapmap];0.87[CHB][hapmap]
rs2860454	0.80[YRI][hapmap]
rs2898950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2920137	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2920140	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2920141	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2920142	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2923946	0.93[LWK][hapmap];0.94[MKK][hapmap]
rs2923947	0.85[EUR][1000 genomes]
rs2923951	0.88[CEU][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2923952	0.84[EUR][1000 genomes]
rs2923954	0.87[EUR][1000 genomes]
rs2959058	0.91[LWK][hapmap];0.85[MKK][hapmap]
rs2959060	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2959061	0.88[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2959064	0.85[EUR][1000 genomes]
rs2959069	0.87[CEU][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs2959071	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2959072	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2959073	0.88[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2959080	0.93[LWK][hapmap];0.96[MKK][hapmap]
rs35695744	0.84[EUR][1000 genomes]
rs3794051	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3794052	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4910595	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910874	0.88[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4910881	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6578440	0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs7109811	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs727152	0.91[LWK][hapmap];0.94[MKK][hapmap]
rs7924858	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7927493	0.85[EUR][1000 genomes]
rs7930739	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7938946	0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7940635	0.81[EUR][1000 genomes]
rs7945918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs894455	1.00[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs894457	0.87[CEU][hapmap];0.88[AMR][1000 genomes]
rs9735835	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No data

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	chr11:4102400-4115200	Weak transcription	Fetal Brain Male	brain
12	chr11:4103000-4115200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:4103200-4115200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr11:4105800-4115200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:4106600-4115400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:4108200-4115000	Weak transcription	NHEK	skin
17	chr11:4108200-4115200	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:4108200-4115200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:4108200-4115400	Weak transcription	Small Intestine	intestine
20	chr11:4108400-4114800	Weak transcription	Pancreas	Pancrea
21	chr11:4108400-4115000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr11:4108400-4115200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:4108400-4115200	Weak transcription	Brain Anterior Caudate	brain
24	chr11:4108600-4115000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:4108600-4115000	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:4108600-4115000	Weak transcription	Psoas Muscle	Psoas
27	chr11:4108800-4115000	Weak transcription	Stomach Mucosa	stomach
28	chr11:4108800-4115200	Weak transcription	Brain Angular Gyrus	brain
29	chr11:4109200-4115000	Weak transcription	HSMM	muscle
30	chr11:4109200-4115000	Weak transcription	Osteobl	bone
31	chr11:4109200-4115200	Weak transcription	HUVEC	blood vessel
32	chr11:4109400-4115000	Weak transcription	HepG2	liver
33	chr11:4109600-4114800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:4110000-4115000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr11:4110000-4115200	Weak transcription	Placenta	Placenta
36	chr11:4110200-4115000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:4110200-4115000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:4111800-4115000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:4111800-4115000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr11:4111800-4115000	Weak transcription	HMEC	breast
41	chr11:4112000-4115000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr11:4112000-4115200	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr11:4112200-4115000	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr11:4112400-4114600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr11:4112600-4115200	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr11:4113000-4115000	Weak transcription	Right Ventricle	heart
47	chr11:4113000-4115400	Weak transcription	Ovary	ovary
48	chr11:4113200-4114800	Weak transcription	Aorta	Aorta
49	chr11:4113200-4114800	Weak transcription	Liver	Liver
50	chr11:4113200-4115000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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