Variant report

Variant	rs7851552
Chromosome Location	chr9:100610652-100610653
allele	A/C
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	CTCF	chr9:100610520-100610670	GM12872	blood:	n/a	n/a
2	CTCF	chr9:100610520-100610670	NHEK	skin:	n/a	n/a
3	BACH1	chr9:100610432-100611011	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTBP2	chr9:100610470-100611525	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr9:100610271-100610750	H1-hESC	embryonic stem cell:	n/a	chr9:100610531-100610538
6	RAD21	chr9:100610384-100610666	H1-hESC	embryonic stem cell:	n/a	chr9:100610531-100610538
7	CTCF	chr9:100610520-100610670	GM12865	blood:	n/a	n/a
8	SUZ12	chr9:100610293-100612160	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr9:100610520-100610670	HCPEpiC	choroid plexus:	n/a	n/a
10	CTCF	chr9:100610580-100610730	HA-sp	spinal cord:	n/a	n/a
11	SUZ12	chr9:100609498-100612500	NT2-D1	testis:	n/a	n/a
12	CTCF	chr9:100610520-100610670	GM12873	blood:	n/a	n/a
13	CTCF	chr9:100610580-100610730	AG04450	lung:	n/a	n/a
14	CTCF	chr9:100610520-100610670	AG10803	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100608561..100611122-chr9:100630030..100632695,2	K562	blood:

Variant related genes	Relation type
FOXE1	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10046805	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113884	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10113907	0.81[AFR][1000 genomes]
rs10117642	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10119760	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10119795	0.82[AFR][1000 genomes]
rs10119853	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10120412	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10122541	0.86[AMR][1000 genomes]
rs10123699	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10759975	0.81[EUR][1000 genomes]
rs10759981	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10818124	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10818133	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818175	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10983958	0.90[ASN][1000 genomes]
rs10983959	0.90[ASN][1000 genomes]
rs10984103	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1156850	0.83[ASN][1000 genomes]
rs12341377	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342417	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12343182	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12347191	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348691	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13287360	0.81[EUR][1000 genomes]
rs13299924	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13300874	0.82[AFR][1000 genomes]
rs13302470	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1443434	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443435	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443436	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1867277	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867278	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867280	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1955143	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955144	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955145	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2120264	0.80[AMR][1000 genomes]
rs2401639	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417575	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2417576	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3021526	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3758248	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758251	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4297160	0.87[ASN][1000 genomes]
rs4460498	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743139	0.81[EUR][1000 genomes]
rs6478437	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478445	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7033315	0.83[AFR][1000 genomes]
rs7033765	0.87[ASN][1000 genomes]
rs7037175	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7043516	0.82[AFR][1000 genomes]
rs7045138	0.87[ASN][1000 genomes]
rs72753507	0.82[AFR][1000 genomes]
rs72753509	0.82[AFR][1000 genomes]
rs7357707	0.83[AFR][1000 genomes]
rs7851660	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860144	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7868534	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7870540	0.83[ASN][1000 genomes]
rs7870795	0.83[ASN][1000 genomes]
rs874004	0.84[AFR][1000 genomes]
rs894673	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907581	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs925487	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs993501	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100609600-100611000	Enhancers	Pancreas	Pancrea
2	chr9:100609600-100611200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
3	chr9:100609800-100610800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:100609800-100611400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr9:100610000-100610800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:100610000-100611000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:100610000-100611200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr9:100610000-100611400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr9:100610000-100611800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr9:100610200-100610800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
11	chr9:100610200-100610800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr9:100610200-100610800	Bivalent Enhancer	HMEC	breast
13	chr9:100610200-100611000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:100610200-100611000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr9:100610200-100611600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr9:100610400-100610800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:100610400-100610800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:100610400-100610800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
19	chr9:100610400-100610800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:100610400-100610800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:100610400-100610800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
22	chr9:100610400-100610800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
23	chr9:100610400-100610800	Flanking Bivalent TSS/Enh	NHEK	skin
24	chr9:100610400-100611000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:100610400-100611000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
26	chr9:100610400-100611000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
27	chr9:100610400-100611000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
28	chr9:100610400-100611000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
29	chr9:100610400-100611000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr9:100610400-100611000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:100610400-100611000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:100610400-100611000	Bivalent Enhancer	Adipose Nuclei	Adipose
33	chr9:100610400-100611000	Bivalent Enhancer	Liver	Liver
34	chr9:100610400-100611000	Bivalent Enhancer	Brain Hippocampus Middle	brain
35	chr9:100610400-100611000	Bivalent Enhancer	Brain Substantia Nigra	brain
36	chr9:100610400-100611000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
37	chr9:100610400-100611000	Bivalent Enhancer	Fetal Brain Female	brain
38	chr9:100610400-100611000	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr9:100610400-100611000	Bivalent Enhancer	HSMM	muscle
40	chr9:100610400-100611200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:100610400-100611200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr9:100610400-100611200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
43	chr9:100610400-100611200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:100610400-100611200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr9:100610400-100611400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
46	chr9:100610400-100611400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:100610400-100611400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
48	chr9:100610400-100611400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr9:100610400-100611400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
50	chr9:100610400-100611400	Bivalent Enhancer	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links