Variant report

Variant	rs4661172
Chromosome Location	chr1:155929859-155929860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155929776..155931816-chr1:155936198..155938525,2	MCF-7	breast:
2	chr1:155902649..155906864-chr1:155928278..155934368,7	MCF-7	breast:
3	chr1:155928147..155930680-chr1:155950511..155952920,2	K562	blood:
4	chr1:155910241..155913815-chr1:155925549..155931886,5	K562	blood:
5	chr1:155929665..155932692-chr1:155935407..155940311,5	MCF-7	breast:
6	chr1:155928325..155931232-chr1:155957996..155960430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116584	Chromatin interaction
ENSG00000173080	Chromatin interaction
ENSG00000132680	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1010033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1018730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1055184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908485	0.97[EUR][1000 genomes]
rs11264421	0.92[EUR][1000 genomes]
rs12039053	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129384	0.83[AFR][1000 genomes]
rs12138833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747344	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1544119	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs1749407	0.89[EUR][1000 genomes]
rs1749408	0.84[EUR][1000 genomes]
rs1749409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1765275	0.85[CEU][hapmap];0.97[EUR][1000 genomes]
rs1964951	0.96[EUR][1000 genomes]
rs2275071	1.00[ASN][1000 genomes]
rs2275079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275081	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2364402	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2364404	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379575	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886069	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34802187	0.99[EUR][1000 genomes]
rs35138477	0.85[EUR][1000 genomes]
rs35374730	0.96[EUR][1000 genomes]
rs35588936	0.89[CEU][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs35730001	0.96[EUR][1000 genomes]
rs3738587	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3768280	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4412586	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4661160	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4661162	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4661170	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs493446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506688	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs527113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs536870	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs572609	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs605025	1.00[CEU][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs6660802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6667096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs708614	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71628697	0.97[EUR][1000 genomes]
rs71628699	0.86[EUR][1000 genomes]
rs822502	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs822503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs822519	0.89[ASW][hapmap];1.00[CEU][hapmap]
rs822653	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155905000-155945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155911200-155940000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:155914800-155930200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:155914800-155931600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:155915200-155930600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:155915200-155936800	Strong transcription	Fetal Brain Female	brain
7	chr1:155915200-155937000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:155915800-155930000	Strong transcription	Left Ventricle	heart
9	chr1:155915800-155930400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:155915800-155930400	Strong transcription	Osteobl	bone
11	chr1:155915800-155930600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:155915800-155931600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:155915800-155935200	Strong transcription	Brain Germinal Matrix	brain
14	chr1:155915800-155936600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:155916000-155930600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:155916000-155931400	Strong transcription	HUVEC	blood vessel
17	chr1:155916000-155937000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:155916200-155930200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:155916200-155931600	Weak transcription	Right Atrium	heart
20	chr1:155916200-155932400	Strong transcription	Colon Smooth Muscle	Colon
21	chr1:155916200-155937000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:155916400-155930400	Strong transcription	Adipose Nuclei	Adipose
23	chr1:155916400-155930600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:155916400-155931800	Strong transcription	Lung	lung
25	chr1:155916400-155936200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:155916400-155936400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr1:155916400-155936600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:155916400-155937200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:155916400-155937400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:155916600-155930000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:155916600-155932400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:155916600-155935800	Strong transcription	Fetal Intestine Small	intestine
33	chr1:155916600-155937000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:155916600-155937200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:155916800-155931600	Strong transcription	Colonic Mucosa	Colon
36	chr1:155916800-155932400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:155916800-155937000	Strong transcription	Thymus	Thymus
38	chr1:155917000-155931800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:155917000-155937200	Strong transcription	Fetal Intestine Large	intestine
40	chr1:155917000-155939400	Strong transcription	Dnd41	blood
41	chr1:155917200-155930400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:155917200-155936800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:155917400-155930000	Strong transcription	Fetal Muscle Leg	muscle
44	chr1:155917400-155931600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:155917400-155931800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:155917600-155930000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:155917600-155930600	Strong transcription	Spleen	Spleen
48	chr1:155917600-155932000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:155917600-155936400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:155917600-155937000	Strong transcription	Fetal Thymus	thymus

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