Variant report

Variant	rs2999511
Chromosome Location	chr1:151946074-151946075
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151941976..151947771-chr1:152006202..152009564,7	MCF-7	breast:
2	chr1:151890104..151891897-chr1:151945321..151946956,2	K562	blood:
3	chr1:151940762..151943209-chr1:151945501..151947443,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1038746	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1038748	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1387834	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1387835	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1473493	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1473494	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473495	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1490191	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1532132	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1552605	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1552607	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1602245	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1602246	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1602248	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17583707	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1826170	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1826171	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1826172	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1844542	0.82[AMR][1000 genomes]
rs1873311	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2087550	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2338018	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2338210	0.82[AMR][1000 genomes]
rs2932563	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932564	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932584	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932585	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932588	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932591	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932592	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932595	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932596	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932597	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999509	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999514	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999518	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999520	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999522	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999523	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999524	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999525	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999527	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999529	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999530	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2999558	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3007692	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3007693	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3007699	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3007700	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3007701	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3007704	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34370890	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61113720	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs971888	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	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
6	nsv2855	chr1:151936470-151966381	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	85 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151934600-151953400	Weak transcription	Psoas Muscle	Psoas
2	chr1:151938400-151946200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:151939600-151950800	Enhancers	Fetal Intestine Small	intestine
4	chr1:151941000-151946200	Weak transcription	Colonic Mucosa	Colon
5	chr1:151941000-151953200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:151941000-151953200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:151941000-151953400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:151941000-151953400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:151941000-151954800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:151941200-151952800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:151941200-151952800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:151941200-151953000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:151941200-151955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:151941400-151947200	Weak transcription	Liver	Liver
15	chr1:151941600-151961200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:151941800-151949400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:151941800-151953000	Weak transcription	Lung	lung
18	chr1:151941800-151953600	Weak transcription	Gastric	stomach
19	chr1:151941800-151956200	Weak transcription	Pancreas	Pancrea
20	chr1:151942400-151951800	Enhancers	Fetal Intestine Large	intestine
21	chr1:151942600-151946800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr1:151943000-151949400	Weak transcription	Esophagus	oesophagus
23	chr1:151943000-151953000	Weak transcription	Spleen	Spleen
24	chr1:151943400-151949000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:151944200-151946200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:151944800-151946200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:151944800-151946200	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr1:151944800-151946600	Enhancers	Fetal Kidney	kidney
29	chr1:151945000-151946200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:151945000-151946200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:151945000-151946200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr1:151945000-151946200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:151945000-151946200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:151945000-151946400	Enhancers	Fetal Brain Male	brain
35	chr1:151945000-151946400	Enhancers	HSMMtube	muscle
36	chr1:151945000-151946600	Flanking Active TSS	A549	lung
37	chr1:151945200-151946200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr1:151945200-151946200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:151945200-151946200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:151945200-151946200	Enhancers	Colon Smooth Muscle	Colon
41	chr1:151945200-151946200	Enhancers	Placenta	Placenta
42	chr1:151945200-151946600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr1:151945200-151946600	Enhancers	Stomach Mucosa	stomach
44	chr1:151945400-151946800	Weak transcription	Adipose Nuclei	Adipose
45	chr1:151945400-151947400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:151945400-151947800	Enhancers	HepG2	liver
47	chr1:151945400-151949200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:151945400-151952400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:151945400-151953400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:151945600-151946200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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