Variant report

Variant	rs2999558
Chromosome Location	chr1:151972510-151972511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151972354..151974327-chr1:152005539..152008524,2	K562	blood:
2	chr1:151961745..151973594-chr1:152015769..152025096,31	MCF-7	breast:
3	chr1:151939119..151942240-chr1:151972408..151975216,4	K562	blood:
4	chr1:151939365..151942240-chr1:151972408..151973945,2	K562	blood:
5	chr1:109234069..109236515-chr1:151971983..151974186,2	MCF-7	breast:
6	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
7	chr1:151905903..151909731-chr1:151970506..151972835,3	MCF-7	breast:
8	chr1:151879889..151882553-chr1:151972066..151974535,2	MCF-7	breast:
9	chr1:151859844..151863422-chr1:151970039..151972808,5	MCF-7	breast:
10	chr1:151823821..151827198-chr1:151970881..151974396,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction
ENSG00000196407	Chromatin interaction
ENSG00000134186	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1003107	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs10158030	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs1038746	1.00[CHB][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1038748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1048910	0.82[AFR][1000 genomes]
rs10788813	1.00[CHB][hapmap]
rs10788814	0.82[AFR][1000 genomes]
rs10788816	1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs10888449	0.87[AFR][1000 genomes]
rs10888453	1.00[CHB][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs11204911	1.00[CHB][hapmap]
rs11204912	1.00[CHB][hapmap]
rs11204923	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578030	1.00[CHB][hapmap]
rs12723616	1.00[CHB][hapmap]
rs1387834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1387835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1473493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1473494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1473495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1490187	1.00[CHB][hapmap]
rs1490188	0.96[ASN][1000 genomes]
rs1490190	0.87[AFR][1000 genomes]
rs1490191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes]
rs1496037	1.00[CHB][hapmap]
rs1532132	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1552605	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1552606	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs1552607	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1602245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1602246	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1602248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17583707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes]
rs1826170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1826171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1826172	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1844542	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1873310	1.00[CHB][hapmap]
rs1873311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1873312	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs1967084	1.00[ASN][1000 genomes]
rs1967085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1979638	1.00[ASN][1000 genomes]
rs2087550	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2130526	0.87[AFR][1000 genomes]
rs2338018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2338203	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs2338204	0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs2338210	0.82[AMR][1000 genomes]
rs2932563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2932564	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2932567	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2932572	0.96[ASN][1000 genomes]
rs2932573	0.96[ASN][1000 genomes]
rs2932578	0.83[AFR][1000 genomes]
rs2932584	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2932585	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2932588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999509	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2999511	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2999514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999515	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999519	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2999520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999522	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999523	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2999524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999525	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999527	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999530	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999535	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2999538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2999551	1.00[CHB][hapmap]
rs2999552	1.00[CHB][hapmap]
rs2999555	1.00[CHB][hapmap]
rs3001979	1.00[CHB][hapmap]
rs3007672	1.00[CHB][hapmap]
rs3007676	1.00[CHB][hapmap]
rs3007679	1.00[CHB][hapmap]
rs3007682	0.83[AFR][1000 genomes]
rs3007690	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs3007692	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3007693	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3007699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3007700	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3007701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3007704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3007714	1.00[ASN][1000 genomes]
rs3122300	1.00[CHB][hapmap]
rs3122301	1.00[CHB][hapmap]
rs3134814	1.00[CHB][hapmap]
rs34370890	0.91[AMR][1000 genomes]
rs3748805	0.87[AFR][1000 genomes]
rs3762427	0.82[AFR][1000 genomes]
rs4845385	1.00[CHB][hapmap];0.89[YRI][hapmap]
rs4845388	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs4845393	1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs4845660	1.00[CHB][hapmap]
rs4845664	1.00[CHB][hapmap]
rs4845699	0.87[AFR][1000 genomes]
rs61113720	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6587626	0.82[ASW][hapmap];1.00[CHB][hapmap]
rs6587628	1.00[CHB][hapmap]
rs6587629	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs6587630	1.00[CHB][hapmap]
rs6587641	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6659029	1.00[CHB][hapmap]
rs6662463	0.82[AFR][1000 genomes]
rs6685291	1.00[CHB][hapmap]
rs6690443	0.82[AFR][1000 genomes]
rs6691350	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs6704157	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7529451	1.00[CHB][hapmap]
rs7532721	1.00[CHB][hapmap]
rs902314	1.00[CHB][hapmap]
rs902315	1.00[CHB][hapmap]
rs959945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs971888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9943225	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs994974	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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151966800-151976800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:151967000-151973000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:151967000-151977000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:151967200-151973200	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:151967200-151974000	Enhancers	HMEC	breast
6	chr1:151967200-151977000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:151967800-151973600	Enhancers	NHEK	skin
8	chr1:151967800-151973800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:151967800-151977200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:151968000-151973000	Weak transcription	Adipose Nuclei	Adipose
11	chr1:151968200-151973000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:151968200-151973200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:151968200-151973400	Weak transcription	HepG2	liver
14	chr1:151968200-151973400	Weak transcription	Osteobl	bone
15	chr1:151968200-151973600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:151968400-151972800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:151968600-151973600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:151968600-151973600	Weak transcription	HSMM	muscle
19	chr1:151968800-151973800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:151969400-151973800	Weak transcription	Placenta	Placenta
21	chr1:151970200-151972600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:151970200-151973000	Weak transcription	NHDF-Ad	bronchial
23	chr1:151970600-151972800	Enhancers	Hela-S3	cervix
24	chr1:151971000-151974400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr1:151971800-151973000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:151971800-151973600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:151971800-151973600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:151972000-151973000	Enhancers	Esophagus	oesophagus
29	chr1:151972000-151973200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:151972000-151973200	Weak transcription	Stomach Mucosa	stomach
31	chr1:151972000-151974200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:151972200-151972600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:151972200-151973800	Weak transcription	Fetal Intestine Small	intestine
34	chr1:151972400-151972600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:151972400-151972600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:151972400-151973200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:151972400-151973800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:151972400-151973800	Weak transcription	Fetal Intestine Large	intestine
39	chr1:151972400-151974400	Enhancers	A549	lung

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