Variant report

Variant	rs1588669
Chromosome Location	chr3:28358954-28358955
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	chr3:27753294..27754202-chr3:28358564..28359259,2	MCF-7	breast:
2	chr3:28303255..28306157-chr3:28357990..28360195,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CMC1-3	chr3:28357824-28361253	NONHSAT088780

Variant related genes	Relation type
ENSG00000187118	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10510610	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11716132	0.88[ASN][1000 genomes]
rs12106746	0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12106806	0.90[AFR][1000 genomes]
rs12107556	0.90[AFR][1000 genomes]
rs12107561	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12374021	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12485652	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12488712	1.00[ASW][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs12491905	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12493720	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12493797	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12495684	1.00[JPT][hapmap]
rs13068978	0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13089663	0.88[ASN][1000 genomes]
rs13095609	1.00[ASW][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13099977	1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1599951	1.00[ASW][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17639954	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1870258	1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2125205	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34335277	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34463163	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34539152	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs34637008	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35194037	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35374336	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs36106945	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4393865	1.00[ASW][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4552313	1.00[ASW][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680912	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56058287	0.88[ASN][1000 genomes]
rs62251110	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62251112	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62251132	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6551254	0.82[ASN][1000 genomes]
rs6786752	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs6799435	0.88[AFR][1000 genomes]
rs6803915	1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs6805638	0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7624015	0.86[AFR][1000 genomes]
rs7624111	0.86[AFR][1000 genomes]
rs9968098	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28314400-28365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:28315000-28363000	Weak transcription	A549	lung
3	chr3:28317600-28380000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
5	chr3:28326400-28365400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:28332800-28360000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:28332800-28360200	Weak transcription	Left Ventricle	heart
8	chr3:28332800-28360400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:28332800-28362400	Weak transcription	Primary B cells from cord blood	blood
10	chr3:28332800-28365200	Weak transcription	HSMMtube	muscle
11	chr3:28332800-28365400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:28336800-28359400	Weak transcription	K562	blood
13	chr3:28337200-28365200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:28337400-28360400	Weak transcription	Liver	Liver
15	chr3:28337400-28361000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:28337400-28363000	Weak transcription	GM12878-XiMat	blood
17	chr3:28337600-28360200	Weak transcription	Fetal Lung	lung
18	chr3:28337600-28360200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:28337600-28361000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:28338000-28359600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:28338000-28360200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:28338000-28360600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:28338200-28364000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:28339600-28359200	Weak transcription	Dnd41	blood
25	chr3:28343800-28383800	Weak transcription	Aorta	Aorta
26	chr3:28347400-28360000	Weak transcription	Fetal Intestine Large	intestine
27	chr3:28348600-28360000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:28348600-28365200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:28349000-28365400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:28349400-28364200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:28349400-28365600	Weak transcription	Psoas Muscle	Psoas
32	chr3:28349600-28365400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:28349800-28359800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:28349800-28389400	Weak transcription	Gastric	stomach
35	chr3:28350000-28359600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr3:28350000-28363800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:28350000-28376800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:28350200-28361600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:28350400-28365400	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:28350600-28360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:28351200-28366600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:28351400-28365600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:28351400-28366800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:28352800-28360000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:28353200-28360200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:28354200-28364600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:28354800-28363000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:28354800-28365600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr3:28355200-28360600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:28355800-28359400	Weak transcription	Primary T cells fromperipheralblood	blood

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