Variant report

Variant	rs72898840
Chromosome Location	chr2:189459013-189459014
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	chr2:189449607..189454566-chr2:189458525..189463315,5	MCF-7	breast:
2	chr2:189457452..189459622-chr2:189465915..189469641,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL3A1-2	chr2:189458667-189459095	NONHSAT076034

Variant related genes	Relation type
ENSG00000144366	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10931353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10931357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10931368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11676244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11676569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11678035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11679949	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11683909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11683969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11684224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11685643	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11693105	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11694636	0.86[EUR][1000 genomes]
rs11695177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12151605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34323074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34587834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57067423	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57210291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58210062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59668663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60162413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60514585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60608780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60894296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61011178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61500341	0.93[EUR][1000 genomes]
rs72896824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72896833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72896844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72896851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72896879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72898830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72898843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72898858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72898866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72898876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898898	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72898900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72900830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72900854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72900855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72900857	0.86[EUR][1000 genomes]
rs72900861	0.86[EUR][1000 genomes]
rs72900862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72900870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72902608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72902633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72902639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72902642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72902649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72902655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72902659	1.00[AMR][1000 genomes]
rs72902678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72902691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72904702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906616	1.00[AMR][1000 genomes]
rs72906620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906646	1.00[AMR][1000 genomes]
rs72909505	1.00[AFR][1000 genomes]
rs72909509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909536	1.00[AMR][1000 genomes]
rs72909549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909559	0.86[EUR][1000 genomes]
rs72909566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72909598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911497	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72911501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72913327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72913360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72913365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7423329	0.80[EUR][1000 genomes]
rs7579593	0.86[EUR][1000 genomes]
rs7579655	0.86[EUR][1000 genomes]

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	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv834489	chr2:189329027-189494224	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv533110	chr2:189354436-189462552	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189420600-189463200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:189431400-189463200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:189433600-189459400	Weak transcription	Psoas Muscle	Psoas
4	chr2:189434400-189463200	Weak transcription	Fetal Intestine Large	intestine
5	chr2:189434400-189465000	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:189436400-189463200	Weak transcription	Ovary	ovary
7	chr2:189443800-189464000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:189445800-189460200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:189445800-189463400	Weak transcription	NHLF	lung
10	chr2:189446200-189461000	Weak transcription	Adipose Nuclei	Adipose
11	chr2:189448600-189459800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:189450200-189459400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:189450200-189463800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:189450400-189462000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:189450400-189463200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:189450400-189470600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:189450400-189475000	Weak transcription	Aorta	Aorta
18	chr2:189450600-189459400	Weak transcription	Fetal Stomach	stomach
19	chr2:189450600-189459600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:189450600-189461400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:189450600-189463400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:189450600-189463400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:189450600-189463800	Weak transcription	Fetal Lung	lung
24	chr2:189450600-189464000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:189450600-189464000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:189450800-189460800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:189452800-189463200	Weak transcription	A549	lung
28	chr2:189453400-189460400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:189453600-189460400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:189453600-189463000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:189453600-189463400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:189455000-189461000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:189455200-189460400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:189455200-189461800	Weak transcription	HUVEC	blood vessel
35	chr2:189455600-189463400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:189458400-189460000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:189458600-189460000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:189458600-189461800	Strong transcription	Placenta	Placenta
39	chr2:189459000-189465400	Enhancers	Pancreatic Islets	Pancreatic Islet

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