Variant report

Variant	rs10017522
Chromosome Location	chr4:106124205-106124206
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106066798..106071531-chr4:106121174..106128252,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10003144	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10006632	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10006721	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018267	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10022126	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022891	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10023701	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10026237	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10027791	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033325	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932794	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11938493	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11941838	1.00[ASN][1000 genomes]
rs11943394	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944001	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11947617	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505746	0.89[ASN][1000 genomes]
rs2017763	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28394039	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655620	0.82[ASN][1000 genomes]
rs28707121	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3733609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235413	0.92[ASN][1000 genomes]
rs55793049	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58862751	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59339947	0.95[ASN][1000 genomes]
rs59806714	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60886348	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826102	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831247	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831445	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833560	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6835030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6857812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955167	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955198	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73836047	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73836048	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73836052	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73836055	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73838074	1.00[ASN][1000 genomes]
rs7662448	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696287	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696337	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698398	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7698522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7700148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871215	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931653	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9985622	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9993497	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9997323	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9998069	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:76 , 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	chr4:106106000-106135000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:106106200-106155000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr4:106106600-106125800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:106111800-106127400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:106112200-106127200	Weak transcription	Primary T cells from cord blood	blood
9	chr4:106112400-106127000	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:106112800-106127400	Weak transcription	Placenta	Placenta
11	chr4:106113000-106126800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:106113000-106127200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:106113000-106154800	Weak transcription	Fetal Thymus	thymus
14	chr4:106113200-106136000	Weak transcription	Brain Anterior Caudate	brain
15	chr4:106113200-106136000	Weak transcription	Brain Substantia Nigra	brain
16	chr4:106113200-106136800	Weak transcription	Fetal Kidney	kidney
17	chr4:106113200-106146600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:106113600-106136000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:106113600-106173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:106113600-106195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:106114400-106129000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:106114400-106136200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:106114400-106155200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:106114600-106127400	Weak transcription	Right Ventricle	heart
25	chr4:106114600-106127400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:106114600-106127400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:106114600-106134400	Weak transcription	Liver	Liver
28	chr4:106114600-106136000	Weak transcription	Pancreas	Pancrea
29	chr4:106114600-106145400	Weak transcription	Adipose Nuclei	Adipose
30	chr4:106114600-106155600	Weak transcription	Esophagus	oesophagus
31	chr4:106116400-106130000	Weak transcription	HMEC	breast
32	chr4:106116400-106131600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:106117600-106136000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:106117800-106124400	Weak transcription	Fetal Lung	lung
35	chr4:106118000-106136200	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:106118000-106136800	Weak transcription	HSMMtube	muscle
37	chr4:106118000-106155400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:106118200-106135600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:106118400-106135800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:106118600-106127000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:106118800-106127000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:106118800-106127000	Weak transcription	Fetal Heart	heart
43	chr4:106118800-106127200	Weak transcription	Left Ventricle	heart
44	chr4:106118800-106127400	Weak transcription	Primary B cells from cord blood	blood
45	chr4:106118800-106128600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:106118800-106131400	Weak transcription	Fetal Intestine Small	intestine
47	chr4:106118800-106131400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr4:106118800-106131600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:106118800-106135000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:106118800-106136000	Weak transcription	NH-A	brain

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