Variant report

Variant	rs2028670
Chromosome Location	chr2:172853809-172853810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172822526..172824288-chr2:172851603..172854588,2	K562	blood:
2	chr2:172851801..172855729-chr2:172948851..172951806,4	K562	blood:
3	chr2:172853366..172855410-chr2:172959572..172961641,2	MCF-7	breast:
4	chr2:172853346..172855729-chr2:172950306..172952134,2	K562	blood:

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10166352	0.80[ASN][1000 genomes]
rs10177679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10179020	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10188587	0.80[ASN][1000 genomes]
rs10191399	0.88[AMR][1000 genomes]
rs10196521	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1022358	1.00[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs10432474	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10439296	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10930497	1.00[CEU][hapmap]
rs10930498	0.80[ASN][1000 genomes]
rs10930500	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10930501	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105264	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11676484	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677573	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11683436	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11692418	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11695887	0.80[ASN][1000 genomes]
rs11883977	0.87[AFR][1000 genomes]
rs11903123	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11903410	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12467010	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12468218	0.80[ASN][1000 genomes]
rs12473516	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478215	0.80[ASN][1000 genomes]
rs12479374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12617265	1.00[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12619137	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12692979	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs13017988	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs13031370	0.83[AMR][1000 genomes]
rs13399316	1.00[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1400816	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1443699	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1443700	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17581715	1.00[CEU][hapmap]
rs1878583	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1982288	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996425	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2028671	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028673	0.84[AMR][1000 genomes]
rs2028674	0.83[AMR][1000 genomes]
rs2056202	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2176466	1.00[JPT][hapmap]
rs2292813	0.80[AMR][1000 genomes]
rs2357064	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2357206	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2357207	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28372952	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770443	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs3770444	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3770453	0.84[ASW][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3770457	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3791343	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821092	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3821094	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3821096	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4072279	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4324292	0.88[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4507064	0.80[AMR][1000 genomes]
rs4668417	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59853867	0.80[ASN][1000 genomes]
rs60706248	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62182438	0.82[ASN][1000 genomes]
rs6433313	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6433315	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6433316	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6433317	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6433318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433322	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6707142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711813	1.00[ASW][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6714214	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726050	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6733123	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6736159	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6740705	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6741030	0.81[AFR][1000 genomes]
rs6742905	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6753551	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6753859	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6757680	1.00[ASW][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6758494	1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs6760680	1.00[JPT][hapmap]
rs718936	1.00[CEU][hapmap]
rs7340516	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7371503	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7371631	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560031	1.00[CEU][hapmap]
rs7579509	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7580132	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs7580232	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7583860	0.82[AMR][1000 genomes]
rs7588025	0.94[ASW][hapmap];1.00[JPT][hapmap]
rs7594478	1.00[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7597525	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598232	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs925881	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs949548	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs970948	0.94[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv821790	chr2:172848378-172854109	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172780600-172854200	Weak transcription	Small Intestine	intestine
2	chr2:172796000-172855200	Weak transcription	Gastric	stomach
3	chr2:172810000-172862600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:172811800-172855600	Weak transcription	Fetal Heart	heart
5	chr2:172813000-172859200	Weak transcription	Fetal Brain Male	brain
6	chr2:172821000-172862800	Weak transcription	Brain Angular Gyrus	brain
7	chr2:172824000-172857800	Weak transcription	Brain Anterior Caudate	brain
8	chr2:172824000-172857800	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:172840800-172857600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:172844000-172854000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:172844200-172857200	Weak transcription	Brain Germinal Matrix	brain
12	chr2:172844400-172857400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:172844600-172855600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:172845200-172857600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:172845600-172854200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:172845600-172854400	Weak transcription	Thymus	Thymus
17	chr2:172845600-172855600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:172846000-172857600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:172847400-172864000	Weak transcription	HSMM	muscle
20	chr2:172847600-172854400	Weak transcription	Fetal Stomach	stomach
21	chr2:172847600-172855000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:172847800-172857600	Weak transcription	Ovary	ovary
23	chr2:172848000-172863200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:172848200-172855600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:172848400-172856000	Weak transcription	K562	blood
26	chr2:172848800-172855200	Weak transcription	Fetal Intestine Large	intestine
27	chr2:172849000-172854000	Weak transcription	Liver	Liver
28	chr2:172849200-172854200	Weak transcription	Fetal Thymus	thymus
29	chr2:172849200-172855000	Weak transcription	Primary T cells from cord blood	blood
30	chr2:172849200-172856600	Weak transcription	Left Ventricle	heart
31	chr2:172849200-172857200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:172849200-172857400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:172849400-172855400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:172849600-172863800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:172850400-172860600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:172851000-172856800	Weak transcription	Dnd41	blood
37	chr2:172851600-172857600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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