Variant report

Variant	rs9993497
Chromosome Location	chr4:106111749-106111750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106064096..106067013-chr4:106110754..106112380,2	MCF-7	breast:
2	chr4:106111372..106113018-chr4:106117335..106120192,2	MCF-7	breast:
3	chr4:106074267..106075814-chr4:106111542..106113452,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGEF38-3	chr4:106111517-106111860	NONHSAT097667

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10003144	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10006632	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10006721	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10008189	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10017522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10018267	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022126	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10022891	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10023701	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10026237	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027791	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10033325	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11932794	0.89[ASN][1000 genomes]
rs11938493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941838	0.92[ASN][1000 genomes]
rs11943394	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11944001	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11944085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11947617	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12505746	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2017763	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28394039	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28707121	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733609	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796927	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4235413	1.00[ASN][1000 genomes]
rs55793049	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58862751	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59339947	0.86[ASN][1000 genomes]
rs59806714	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60886348	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6826102	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6831247	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6831445	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6833560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835030	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6839609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6843141	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6857812	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72955167	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72955198	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73836047	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73836048	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73836052	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73836055	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73838074	0.92[ASN][1000 genomes]
rs7662448	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7696287	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7696337	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7698398	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698522	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7700148	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs871215	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs931653	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9985622	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997323	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9998069	1.00[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:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106069400-106114200	Weak transcription	Esophagus	oesophagus
2	chr4:106077000-106112000	Weak transcription	Aorta	Aorta
3	chr4:106078000-106112800	Weak transcription	Fetal Kidney	kidney
4	chr4:106084800-106127400	Weak transcription	Brain Germinal Matrix	brain
5	chr4:106085600-106112800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:106093800-106112400	Weak transcription	Primary B cells from cord blood	blood
7	chr4:106094000-106112600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:106098200-106113200	Weak transcription	Fetal Stomach	stomach
9	chr4:106099000-106114200	Weak transcription	Gastric	stomach
10	chr4:106101000-106146600	Weak transcription	Spleen	Spleen
11	chr4:106101200-106112600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:106101200-106112800	Weak transcription	NHDF-Ad	bronchial
13	chr4:106101400-106112200	Weak transcription	Right Atrium	heart
14	chr4:106101600-106112800	Weak transcription	HSMM	muscle
15	chr4:106102600-106112800	Weak transcription	HSMMtube	muscle
16	chr4:106102600-106113400	Weak transcription	K562	blood
17	chr4:106102800-106127400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:106103600-106112200	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:106104800-106117400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:106105200-106117800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:106106000-106112800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:106106000-106135000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:106106200-106112200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:106106200-106112400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:106106200-106112600	Weak transcription	Brain Anterior Caudate	brain
26	chr4:106106200-106112600	Weak transcription	Fetal Lung	lung
27	chr4:106106200-106112800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:106106200-106112800	Weak transcription	Brain Substantia Nigra	brain
29	chr4:106106200-106112800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:106106200-106114000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:106106200-106114200	Weak transcription	Small Intestine	intestine
32	chr4:106106200-106118600	Weak transcription	Thymus	Thymus
33	chr4:106106200-106155000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr4:106106400-106111800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:106106400-106112800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:106106600-106112600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:106106600-106125800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr4:106107600-106112200	Weak transcription	Right Ventricle	heart
39	chr4:106108000-106112800	Weak transcription	Ovary	ovary
40	chr4:106108000-106115400	Weak transcription	HMEC	breast
41	chr4:106108000-106123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:106108200-106112800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:106108200-106112800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:106108400-106112200	Weak transcription	Left Ventricle	heart
45	chr4:106108400-106112400	Weak transcription	Osteobl	bone
46	chr4:106108400-106112600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:106108400-106112600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr4:106108400-106112600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:106108400-106112600	Weak transcription	NH-A	brain
50	chr4:106108400-106112800	Weak transcription	HUVEC	blood vessel

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