Variant report

Variant	rs9985622
Chromosome Location	chr4:106115292-106115293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106064689..106068216-chr4:106113083..106116896,4	MCF-7	breast:
2	chr4:106114330..106115965-chr4:106120710..106122443,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10003144	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10006632	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10006721	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10008189	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10017522	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10018267	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022126	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10022891	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10023701	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10026237	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027791	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10033325	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11932794	0.89[ASN][1000 genomes]
rs11938493	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941838	0.92[ASN][1000 genomes]
rs11943394	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11944001	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11944085	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11947617	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12505746	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2017763	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28394039	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28707121	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733609	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796927	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4235413	1.00[ASN][1000 genomes]
rs55793049	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58862751	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59339947	0.86[ASN][1000 genomes]
rs59806714	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60886348	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6826102	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6831247	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6831445	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6833560	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835030	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6839609	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6843141	0.92[ASN][1000 genomes]
rs6857812	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72955167	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72955198	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73836047	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73836048	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73836052	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73836055	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73838074	0.92[ASN][1000 genomes]
rs7662448	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7696287	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7696337	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7698398	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698522	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7700148	0.92[ASN][1000 genomes]
rs871215	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs931653	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9993497	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998069	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106084800-106127400	Weak transcription	Brain Germinal Matrix	brain
2	chr4:106101000-106146600	Weak transcription	Spleen	Spleen
3	chr4:106102800-106127400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:106104800-106117400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:106105200-106117800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:106106000-106135000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:106106200-106118600	Weak transcription	Thymus	Thymus
8	chr4:106106200-106155000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:106106600-106125800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:106108000-106115400	Weak transcription	HMEC	breast
11	chr4:106108000-106123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:106110600-106118600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:106111000-106118800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:106111200-106117200	Genic enhancers	Primary monocytes fromperipheralblood	blood
15	chr4:106111800-106127400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:106112200-106127200	Weak transcription	Primary T cells from cord blood	blood
17	chr4:106112400-106115400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:106112400-106115600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:106112400-106116600	Enhancers	Osteobl	bone
20	chr4:106112400-106127000	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:106112600-106117000	Genic enhancers	Monocytes-CD14+_RO01746	blood
22	chr4:106112800-106116400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:106112800-106116400	Enhancers	NHDF-Ad	bronchial
24	chr4:106112800-106116400	Enhancers	NHEK	skin
25	chr4:106112800-106127400	Weak transcription	Placenta	Placenta
26	chr4:106113000-106115400	Genic enhancers	GM12878-XiMat	blood
27	chr4:106113000-106115600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:106113000-106118000	Weak transcription	Ovary	ovary
29	chr4:106113000-106120400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:106113000-106126800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:106113000-106127200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:106113000-106154800	Weak transcription	Fetal Thymus	thymus
33	chr4:106113200-106116200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:106113200-106136000	Weak transcription	Brain Anterior Caudate	brain
35	chr4:106113200-106136000	Weak transcription	Brain Substantia Nigra	brain
36	chr4:106113200-106136800	Weak transcription	Fetal Kidney	kidney
37	chr4:106113200-106146600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:106113400-106117000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr4:106113400-106120600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:106113400-106123800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:106113600-106115400	Weak transcription	NH-A	brain
42	chr4:106113600-106115600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:106113600-106116000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr4:106113600-106117200	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:106113600-106117400	Weak transcription	Fetal Intestine Small	intestine
46	chr4:106113600-106117800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr4:106113600-106136000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:106113600-106173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:106113600-106195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:106114000-106115400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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