Variant report

Variant	rs1858229
Chromosome Location	chr3:156376952-156376953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156371088..156373654-chr3:156376805..156378893,2	K562	blood:
2	chr3:156376696..156378719-chr3:156391982..156394592,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-7	chr3:156359231-156383752	predAs_chen_BG181400_1

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs11710516	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11926558	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11926561	0.86[ASN][1000 genomes]
rs13073605	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13097957	0.86[ASN][1000 genomes]
rs1355280	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1397194	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1397195	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1510269	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1510270	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs168245	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs168295	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs180746	0.83[EUR][1000 genomes]
rs180747	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs182935	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs182936	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs184677	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs186928	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs193198	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs193423	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2054881	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2129909	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2136691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2136692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs237245	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs237246	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2665390	1.00[JPT][hapmap]
rs343991	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs343995	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs343996	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs343997	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs343998	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344000	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344001	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344005	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344006	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs344008	1.00[JPT][hapmap]
rs344009	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344010	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344011	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344012	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344013	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344014	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344015	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344016	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344017	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344023	0.83[EUR][1000 genomes]
rs344029	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344032	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs344047	0.83[EUR][1000 genomes]
rs344048	0.83[EUR][1000 genomes]
rs344049	0.83[EUR][1000 genomes]
rs344050	0.83[EUR][1000 genomes]
rs344052	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344053	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344054	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344055	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344058	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344059	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs344060	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344061	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344062	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344063	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs344064	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344065	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344066	1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344068	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344069	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344070	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs345987	0.83[AMR][1000 genomes]
rs419287	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs427384	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4429586	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4679784	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680296	0.85[AMR][1000 genomes]
rs4680297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5012666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441088	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6441089	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6441092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6441094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6441095	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6799457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7636366	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7640593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs871232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs871233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs907063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs931990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs978108	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs978109	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9823112	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9833951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9841047	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs985854	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9877043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156375000-156378600	Weak transcription	GM12878-XiMat	blood
2	chr3:156375400-156377400	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr3:156375400-156377600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:156375600-156381800	Weak transcription	K562	blood
5	chr3:156376200-156377400	Enhancers	HSMMtube	muscle
6	chr3:156376200-156377600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:156376600-156377400	Enhancers	Psoas Muscle	Psoas
8	chr3:156376600-156377600	Enhancers	Brain Germinal Matrix	brain
9	chr3:156376600-156382400	Weak transcription	Fetal Kidney	kidney
10	chr3:156376600-156383800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:156376600-156385600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:156376800-156377400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr3:156376800-156377600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:156376800-156377600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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