Variant report

Variant	rs1561722
Chromosome Location	chr4:102248391-102248392
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	chr4:102242973..102245664-chr4:102246576..102249048,2	MCF-7	breast:
2	chr4:102244312..102246286-chr4:102248183..102250301,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1011849	0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11943655	0.82[AMR][1000 genomes]
rs11946103	0.82[AMR][1000 genomes]
rs1372243	0.92[AFR][1000 genomes]
rs1372244	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs1441431	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1441434	0.82[AMR][1000 genomes]
rs17031168	0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031172	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031175	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031176	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031180	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs17031182	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs3789755	0.80[AFR][1000 genomes]
rs3974659	0.99[AFR][1000 genomes]
rs4488940	0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4504259	0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4637408	0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs55667372	0.97[AFR][1000 genomes]
rs58629361	0.97[AFR][1000 genomes]
rs59079781	0.92[AFR][1000 genomes]
rs59224049	0.97[AFR][1000 genomes]
rs59763039	0.97[AFR][1000 genomes]
rs60438397	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs60984918	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6532924	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs6532925	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6532926	0.95[AFR][1000 genomes]
rs6810812	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs6812094	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6817805	0.82[AFR][1000 genomes]
rs6827528	0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6828025	0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6830390	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6831471	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs6831824	0.82[AFR][1000 genomes]
rs6832020	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs6834721	0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6837858	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs6842191	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs6844844	0.93[AFR][1000 genomes]
rs6846554	0.84[YRI][hapmap];0.92[AFR][1000 genomes]
rs6852282	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs73835916	0.82[AMR][1000 genomes]
rs73835923	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73835924	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73835931	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73835933	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73835934	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73835935	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835936	0.93[AFR][1000 genomes]
rs73835937	0.99[AFR][1000 genomes]
rs73835938	0.99[AFR][1000 genomes]
rs73835939	0.97[AFR][1000 genomes]
rs73835940	0.97[AFR][1000 genomes]
rs73835941	0.97[AFR][1000 genomes]
rs73835943	0.97[AFR][1000 genomes]
rs73835944	0.81[AFR][1000 genomes]
rs7655806	0.82[AMR][1000 genomes]
rs7661895	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7664396	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7671524	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	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 miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	esv2602939	chr4:102247164-102248757	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102228200-102249400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:102228200-102250400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:102243200-102249200	Weak transcription	Adipose Nuclei	Adipose
4	chr4:102243200-102249200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:102243200-102251600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:102243200-102251800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:102243400-102251000	Enhancers	Primary B cells from peripheral blood	blood
8	chr4:102243400-102252000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:102243400-102256000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:102243600-102251800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:102243600-102256800	Weak transcription	Aorta	Aorta
12	chr4:102243800-102248800	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:102244000-102258000	Weak transcription	Brain Angular Gyrus	brain
14	chr4:102244400-102248600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:102244800-102248800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:102245400-102251200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr4:102245400-102251600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr4:102245600-102249200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr4:102245600-102251800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr4:102245600-102252800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr4:102245600-102255000	Weak transcription	Ovary	ovary
22	chr4:102245800-102252000	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr4:102246400-102249600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr4:102246800-102249400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:102247200-102249000	Enhancers	Primary T cells from cord blood	blood
26	chr4:102247200-102251000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr4:102247400-102249200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:102247400-102249200	Weak transcription	Psoas Muscle	Psoas
29	chr4:102247400-102251600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:102247600-102248800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr4:102247800-102248400	Weak transcription	Primary B cells from cord blood	blood
32	chr4:102247800-102248800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:102247800-102249000	Enhancers	GM12878-XiMat	blood
34	chr4:102247800-102249200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:102247800-102249400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr4:102247800-102249800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:102247800-102251000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr4:102247800-102251200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr4:102247800-102251800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:102248000-102249200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:102248000-102249200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr4:102248000-102250400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:102248000-102250400	Weak transcription	Brain Anterior Caudate	brain
44	chr4:102248000-102250800	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:102248000-102252000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:102248000-102252200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr4:102248200-102249600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:102248200-102250400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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