Variant report

Variant	rs61701375
Chromosome Location	chr9:110044372-110044373
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:110044257-110047284	HepG2	liver:	n/a	n/a
2	CEBPB	chr9:110044341-110044539	K562	blood:	n/a	n/a
3	MYC	chr9:110044291-110044480	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr9:110044294-110047293	IMR90	lung:	n/a	n/a
5	POLR2A	chr9:110042878-110046762	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr9:110044350-110044464	HepG2	liver:	n/a	n/a
7	POLR2A	chr9:110044361-110047198	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:110042843..110044728-chr9:110074492..110076234,2	K562	blood:
2	chr9:110044300..110048942-chr9:110067094..110074281,11	MCF-7	breast:

Variant related genes	Relation type
RAD23B	TF binding region
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10113916	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119641	0.93[ASN][1000 genomes]
rs10122970	0.92[ASN][1000 genomes]
rs10481632	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10521083	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10739234	0.92[AFR][1000 genomes]
rs10739236	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739238	0.92[AFR][1000 genomes]
rs10816474	0.85[AMR][1000 genomes]
rs10816477	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10816480	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10816485	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816490	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816491	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10978767	0.85[AMR][1000 genomes]
rs10978775	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10978776	0.92[ASN][1000 genomes]
rs10978777	0.92[ASN][1000 genomes]
rs10978791	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12342066	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12345455	0.92[ASN][1000 genomes]
rs12555417	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1535765	0.85[AFR][1000 genomes]
rs1805329	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1886134	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1969798	0.80[AFR][1000 genomes]
rs1980725	0.80[AFR][1000 genomes]
rs2005143	0.86[ASN][1000 genomes]
rs2147071	0.85[AFR][1000 genomes]
rs2417776	0.92[ASN][1000 genomes]
rs2417784	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28534368	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28769087	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28848858	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4278207	0.81[EUR][1000 genomes]
rs4625087	0.84[AFR][1000 genomes]
rs4978404	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4978406	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4978849	0.92[AFR][1000 genomes]
rs698475	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7025563	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7029997	0.85[AFR][1000 genomes]
rs7030169	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7030555	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7030631	0.85[AFR][1000 genomes]
rs7031906	0.80[AFR][1000 genomes]
rs7035611	0.92[AFR][1000 genomes]
rs7036284	0.92[ASN][1000 genomes]
rs7038737	0.92[AFR][1000 genomes]
rs7039041	0.92[AFR][1000 genomes]
rs7040217	1.00[ASN][1000 genomes]
rs7041137	1.00[ASN][1000 genomes]
rs7041497	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7043962	0.86[AFR][1000 genomes]
rs7046950	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7856227	0.92[AFR][1000 genomes]
rs7867544	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7873745	0.90[ASN][1000 genomes]
rs817836	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs817838	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs817839	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs817840	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs817841	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs817843	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs817844	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs817845	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs817846	0.88[AFR][1000 genomes]
rs817847	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs817849	0.84[ASN][1000 genomes]
rs817851	0.84[ASN][1000 genomes]
rs942291	0.92[ASN][1000 genomes]
rs942293	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9632893	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9969728	0.92[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	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893698	chr9:109998563-110052660	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110035600-110044600	Enhancers	Placenta	Placenta
2	chr9:110036400-110044400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:110038000-110044400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:110038000-110044400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:110038000-110044400	Weak transcription	NH-A	brain
6	chr9:110039600-110044400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:110039800-110044400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:110039800-110044400	Weak transcription	Adipose Nuclei	Adipose
9	chr9:110039800-110044400	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:110039800-110044400	Weak transcription	A549	lung
11	chr9:110040400-110044400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:110040400-110044400	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:110040400-110044600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:110040400-110044600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr9:110040400-110044600	Weak transcription	Fetal Stomach	stomach
16	chr9:110042200-110044400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:110042200-110044400	Enhancers	NHEK	skin
18	chr9:110042200-110044600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:110042200-110044600	Enhancers	HMEC	breast
20	chr9:110042400-110044400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:110042600-110044600	Enhancers	Fetal Intestine Large	intestine
22	chr9:110042800-110044800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:110043000-110044400	Enhancers	Fetal Intestine Small	intestine
24	chr9:110043000-110044600	Enhancers	Primary B cells from peripheral blood	blood
25	chr9:110043000-110044600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr9:110043000-110044800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:110043200-110044400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:110043200-110044400	Enhancers	GM12878-XiMat	blood
29	chr9:110043400-110044400	Weak transcription	NHDF-Ad	bronchial
30	chr9:110043400-110044400	Weak transcription	Osteobl	bone
31	chr9:110043400-110044600	Weak transcription	Psoas Muscle	Psoas
32	chr9:110043400-110045200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr9:110043600-110044400	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr9:110043600-110044400	Enhancers	Primary hematopoietic stem cells	blood
35	chr9:110043600-110044400	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr9:110043600-110045000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr9:110043800-110044600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr9:110044000-110044400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr9:110044000-110044400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:110044000-110044400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr9:110044000-110044400	Enhancers	K562	blood
42	chr9:110044000-110044400	Enhancers	NHLF	lung
43	chr9:110044000-110044600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr9:110044000-110044600	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr9:110044000-110044600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:110044000-110044600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:110044000-110044600	Enhancers	Brain Germinal Matrix	brain
48	chr9:110044000-110044600	Enhancers	HSMM	muscle
49	chr9:110044200-110044400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:110044200-110044400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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