Variant report

Variant	rs2001270
Chromosome Location	chr1:184493884-184493885
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	chr1:184487281..184489460-chr1:184493042..184495874,2	MCF-7	breast:
2	chr1:184491617..184495454-chr1:184495867..184499341,4	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1007224	0.88[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs10737253	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10797971	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10797972	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10797977	0.80[AMR][1000 genomes]
rs10911606	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap]
rs11588922	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125349	0.94[ASN][1000 genomes]
rs12127674	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1339563	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1339564	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1339565	0.94[ASN][1000 genomes]
rs1339566	0.81[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap]
rs1339567	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1416751	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1569842	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1884200	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2038307	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2038308	0.88[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs2180073	0.81[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap]
rs2180077	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2207528	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2378888	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2890015	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4650667	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4651208	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs4651210	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs4651211	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4651216	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4651217	0.94[ASN][1000 genomes]
rs4651219	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs55729410	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6661707	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6666704	0.84[ASN][1000 genomes]
rs7517518	0.84[ASN][1000 genomes]
rs7520690	0.85[EUR][1000 genomes]
rs7533466	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7544240	0.94[ASN][1000 genomes]
rs9633308	0.92[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9970984	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9970990	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2001270	IVNS1ABP	cis	lymphoblastoid	seeQTL
rs2001270	SLC22A11	trans	parietal	SCAN
rs2001270	ABL2	cis	parietal	SCAN
rs2001270	TDRD5	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184456400-184502200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:184461600-184502800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:184474400-184505400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:184477400-184494800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:184477400-184502200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:184478400-184505200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:184478600-184501200	Weak transcription	Fetal Heart	heart
8	chr1:184478800-184502200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:184480000-184495000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:184480200-184505200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:184480600-184501400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:184481400-184504000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:184483400-184504000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:184483800-184500800	Weak transcription	Left Ventricle	heart
15	chr1:184484000-184503000	Weak transcription	NHDF-Ad	bronchial
16	chr1:184484000-184504000	Weak transcription	NHLF	lung
17	chr1:184485800-184504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:184486800-184505400	Weak transcription	Fetal Intestine Large	intestine
19	chr1:184488800-184496000	Weak transcription	Psoas Muscle	Psoas
20	chr1:184488800-184496000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:184489800-184503800	Weak transcription	HSMMtube	muscle
22	chr1:184489800-184505400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:184492200-184500600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:184492200-184502800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:184492800-184501800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:184493000-184494000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:184493400-184494000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:184493800-184494000	Enhancers	Ovary	ovary

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