Variant report

Variant	rs12404644
Chromosome Location	chr1:185105892-185105893
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185104278..185107115-chr1:185121320..185123089,2	K562	blood:
2	chr1:185099798..185103088-chr1:185104012..185107773,3	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1008502	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1046592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489580	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10489581	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10737256	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs10797997	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs10797998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797999	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10798000	0.86[CHB][hapmap]
rs10911673	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10911674	1.00[ASW][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10911676	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911682	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911686	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12022419	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12023744	0.80[EUR][1000 genomes]
rs12025995	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12026000	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12028809	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12030554	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12030778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12030967	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12031837	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12035073	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12035433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12037466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12037692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12038919	1.00[ASW][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12039541	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12039657	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12040650	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs12041374	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12043427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12043495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12043561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12043617	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12044161	1.00[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12044997	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12045772	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12046095	0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12046202	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12046801	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12049293	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12086086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094983	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs12401293	0.87[EUR][1000 genomes]
rs12404187	0.86[CHB][hapmap]
rs12408279	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12408500	0.83[EUR][1000 genomes]
rs12409926	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1322646	0.91[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs1407554	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1407555	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs1407557	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs1544052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1591585	0.86[CHB][hapmap]
rs16823740	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16865296	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1884447	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2057222	0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2146329	0.86[CHB][hapmap]
rs2273881	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2378958	1.00[ASW][hapmap];0.89[LWK][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3766720	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs3766723	1.00[CEU][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes]
rs3806243	1.00[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs41264588	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41264590	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56107433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61125463	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61495015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6424971	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs6424972	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs6660169	0.86[CHB][hapmap]
rs6673303	0.86[CHB][hapmap]
rs6700484	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs72724103	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72724108	0.81[EUR][1000 genomes]
rs72739693	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72739698	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72739699	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs72741807	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72741808	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72741816	0.83[EUR][1000 genomes]
rs72741819	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7512290	0.86[CHB][hapmap]
rs7519019	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs7533198	0.86[CHB][hapmap]

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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv872588	chr1:185081903-185117688	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv548397	chr1:185104842-185123630	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185056200-185124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:185059000-185124800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:185068400-185110200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:185073600-185115000	Weak transcription	NH-A	brain
5	chr1:185082600-185125400	Weak transcription	Spleen	Spleen
6	chr1:185084200-185124400	Weak transcription	Right Ventricle	heart
7	chr1:185085000-185121400	Weak transcription	NHEK	skin
8	chr1:185085400-185125000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:185086000-185107000	Strong transcription	Liver	Liver
10	chr1:185086000-185120200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:185087000-185125000	Weak transcription	Gastric	stomach
12	chr1:185087600-185117000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:185088000-185107800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:185088200-185120600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:185088600-185106400	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:185089400-185124400	Weak transcription	Colonic Mucosa	Colon
17	chr1:185089600-185121400	Weak transcription	Stomach Mucosa	stomach
18	chr1:185091200-185121400	Weak transcription	Fetal Heart	heart
19	chr1:185093800-185113400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:185093800-185117400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:185094000-185110800	Weak transcription	Brain Angular Gyrus	brain
22	chr1:185094000-185113000	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:185094200-185116600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:185094200-185118400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:185096600-185121400	Weak transcription	Hela-S3	cervix
26	chr1:185100000-185110800	Weak transcription	NHLF	lung
27	chr1:185100400-185106400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:185100800-185111200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:185101000-185106200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr1:185101000-185121000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:185101200-185106600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:185101200-185107000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:185101400-185107000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:185101400-185108600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:185101600-185125200	Weak transcription	Esophagus	oesophagus
36	chr1:185101800-185120200	Strong transcription	Adipose Nuclei	Adipose
37	chr1:185101800-185120800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:185102000-185120800	Strong transcription	Placenta	Placenta
39	chr1:185102200-185109200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:185102400-185108800	Strong transcription	Left Ventricle	heart
41	chr1:185102400-185110600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:185102400-185113400	Weak transcription	HUVEC	blood vessel
43	chr1:185102400-185120600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:185102400-185121400	Weak transcription	HMEC	breast
45	chr1:185102400-185124400	Weak transcription	Brain Germinal Matrix	brain
46	chr1:185102600-185106400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:185102600-185106600	Weak transcription	HSMM	muscle
48	chr1:185102600-185108400	Weak transcription	Fetal Kidney	kidney
49	chr1:185102600-185124400	Weak transcription	Fetal Brain Male	brain
50	chr1:185102600-185124400	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links