Variant report

Variant	rs9646839
Chromosome Location	chr2:209221935-209221936
allele	C/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	CTCF	chr2:209221920-209222070	A549	lung:	n/a	n/a
2	POLR2A	chr2:209221887-209222020	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:209220629..209223614-chr2:209226035..209228837,2	MCF-7	breast:

Variant related genes	Relation type
PTH2R	TF binding region
ENSG00000213081	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10171006	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10175739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10182087	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10186531	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10197824	0.82[AFR][1000 genomes]
rs10197951	0.83[AFR][1000 genomes]
rs10197958	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10201702	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10208004	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10208191	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208295	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210393	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1057390	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10804168	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10932256	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10932259	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11677618	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11691208	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11691313	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11693993	0.94[ASN][1000 genomes]
rs11695873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11897897	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12479282	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12617521	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12618837	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12621871	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12623816	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12694105	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12694109	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12694111	0.80[AMR][1000 genomes]
rs13392540	0.86[CHB][hapmap]
rs1370370	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1370375	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1370377	1.00[JPT][hapmap]
rs1437414	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1465803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1465804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1469941	1.00[ASN][1000 genomes]
rs1529976	0.81[AFR][1000 genomes]
rs1529979	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1561240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1595329	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16840798	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs16840864	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16841092	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16841231	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap]
rs16841233	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16841234	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16841242	0.88[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap]
rs1866044	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1866045	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1898436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1898437	0.85[ASN][1000 genomes]
rs2044457	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2118295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2118296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2118297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2304544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2363468	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2363469	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2363579	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2885786	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3856350	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4462735	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4499359	0.82[AFR][1000 genomes]
rs4673390	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4673392	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4673395	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4673396	0.84[AFR][1000 genomes]
rs4675748	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4675750	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4675751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4675754	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4675755	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4675757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675760	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675761	0.94[ASN][1000 genomes]
rs57553077	1.00[ASN][1000 genomes]
rs59149007	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435441	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6435443	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6435444	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6435445	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6435446	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6435450	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6435452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708926	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6709286	0.80[AFR][1000 genomes]
rs6711933	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6713477	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6718402	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6721780	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725932	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733607	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6734963	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6742461	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6751982	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6758207	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355562	0.94[ASN][1000 genomes]
rs7569723	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7574324	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7580715	1.00[TSI][hapmap]
rs7581075	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7583022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7592472	0.94[ASN][1000 genomes]
rs893253	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs893254	0.80[AFR][1000 genomes]
rs893255	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs893256	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9283521	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9288394	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs934712	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs934714	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs959660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs959855	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs962595	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs976247	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs994696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs994697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv875752	chr2:209141066-209235373	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv437315	chr2:209204714-209249613	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv460055	chr2:209208115-209221935	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv584302	chr2:209208115-209221935	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209147400-209225600	Weak transcription	Stomach Mucosa	stomach
2	chr2:209180600-209224600	Strong transcription	Fetal Thymus	thymus
3	chr2:209182400-209224200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:209185600-209224000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:209188400-209223400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:209188800-209222200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:209188800-209222400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:209188800-209222600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:209188800-209223600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:209188800-209223800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:209188800-209224000	Strong transcription	Primary B cells from cord blood	blood
12	chr2:209188800-209224000	Strong transcription	Primary hematopoietic stem cells	blood
13	chr2:209188800-209224200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:209188800-209224400	Strong transcription	Dnd41	blood
15	chr2:209190600-209224200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:209191200-209224200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:209195400-209223800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:209198000-209224600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:209205400-209223600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:209206600-209223800	Weak transcription	Psoas Muscle	Psoas
21	chr2:209206600-209224200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:209206600-209225400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:209212000-209223600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:209215000-209225400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:209215200-209223800	Strong transcription	GM12878-XiMat	blood
26	chr2:209215200-209224400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:209215400-209222000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:209215400-209224400	Strong transcription	Primary T cells from cord blood	blood
29	chr2:209215800-209222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:209216800-209225000	Weak transcription	Spleen	Spleen
31	chr2:209216800-209226800	Weak transcription	Brain Germinal Matrix	brain
32	chr2:209217000-209223800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:209217000-209224200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:209217000-209225800	Weak transcription	Lung	lung
35	chr2:209217200-209223600	Weak transcription	Fetal Stomach	stomach
36	chr2:209217200-209225000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:209218800-209225400	Weak transcription	Fetal Brain Male	brain
38	chr2:209219400-209225200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:209219400-209228000	Weak transcription	Hela-S3	cervix
40	chr2:209220000-209227600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:209220000-209228000	Weak transcription	NHEK	skin
42	chr2:209220200-209222000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:209220200-209222400	Weak transcription	Ovary	ovary
44	chr2:209220200-209222800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:209220200-209223400	Weak transcription	Brain Angular Gyrus	brain
46	chr2:209220200-209223600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr2:209220200-209223600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:209220200-209223600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:209220200-209223600	Weak transcription	Fetal Heart	heart
50	chr2:209220200-209223600	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links