Variant report

Variant	rs4977753
Chromosome Location	chr9:22030027-22030028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:21991860..21994281-chr9:22027750..22030080,2	MCF-7	breast:
2	chr9:22006075..22010521-chr9:22028543..22032768,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147883	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10115049	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120688	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10120806	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10738605	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10757263	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757264	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10757265	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10757266	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10757267	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10811640	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811643	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811644	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811645	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10965212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10965215	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10965219	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1333035	0.81[AFR][1000 genomes]
rs1333036	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1360590	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1591136	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2106119	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2106120	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2151280	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2383204	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2811712	0.82[AFR][1000 genomes]
rs3218005	0.82[AFR][1000 genomes]
rs3218007	0.82[AFR][1000 genomes]
rs3218012	0.84[EUR][1000 genomes]
rs490005	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs496892	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504318	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567453	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581876	0.90[ASN][1000 genomes]
rs643319	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7027048	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7027950	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7028570	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7035484	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044859	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7049105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944799	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1018514	chr9:21944275-22075326	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv892747	chr9:21984661-22068646	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22009800-22030200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:22009800-22037000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:22022800-22032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:22025000-22033800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:22025400-22039800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:22028800-22030400	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr9:22029000-22032400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr9:22029200-22030400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:22029200-22031800	Strong transcription	Dnd41	blood
10	chr9:22029400-22030200	Enhancers	Primary B cells from cord blood	blood
11	chr9:22029400-22030400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:22029400-22030400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr9:22029400-22030400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr9:22029400-22030600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:22029400-22030800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:22029400-22030800	Enhancers	NHDF-Ad	bronchial
17	chr9:22029400-22031000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr9:22029400-22031000	Enhancers	Hela-S3	cervix
19	chr9:22029400-22031000	Enhancers	HUVEC	blood vessel
20	chr9:22029400-22032600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:22029400-22034200	Enhancers	HMEC	breast
22	chr9:22029800-22031000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr9:22030000-22030400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr9:22030000-22030400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr9:22030000-22030400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr9:22030000-22030400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:22030000-22030400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:22030000-22030400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:22030000-22030400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:22030000-22030600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr9:22030000-22030600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:22030000-22030600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr9:22030000-22030600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr9:22030000-22030600	Enhancers	Duodenum Mucosa	Duodenum
35	chr9:22030000-22030800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:22030000-22030800	Enhancers	Fetal Intestine Small	intestine
37	chr9:22030000-22030800	Enhancers	GM12878-XiMat	blood
38	chr9:22030000-22030800	Enhancers	NH-A	brain
39	chr9:22030000-22030800	Enhancers	Osteobl	bone
40	chr9:22030000-22031000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:22030000-22034200	Enhancers	NHEK	skin

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