Variant report

Variant	rs2366088
Chromosome Location	chr3:164050984-164050985
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	chr3:164050649..164051226-chr3:164523700..164524566,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10936414	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11714036	0.88[ASN][1000 genomes]
rs11717385	0.88[ASN][1000 genomes]
rs12053977	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054354	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486292	0.87[ASN][1000 genomes]
rs12487948	0.88[ASN][1000 genomes]
rs12488423	0.86[ASN][1000 genomes]
rs12491407	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12491958	0.88[ASN][1000 genomes]
rs12492246	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12495540	0.86[ASN][1000 genomes]
rs12495977	0.84[ASN][1000 genomes]
rs12496516	0.83[ASN][1000 genomes]
rs12496876	0.82[ASN][1000 genomes]
rs12632594	0.88[ASN][1000 genomes]
rs1321549	0.86[ASN][1000 genomes]
rs1407078	0.88[ASN][1000 genomes]
rs1449927	0.82[AFR][1000 genomes]
rs1590223	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16847708	0.82[AFR][1000 genomes]
rs16847815	0.88[ASN][1000 genomes]
rs1955378	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2366086	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366087	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34424956	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4473557	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60735329	0.86[ASN][1000 genomes]
rs62280855	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7429375	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877820	chr3:163557163-164167085	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv877825	chr3:163620918-164126802	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877833	chr3:163761825-164109377	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1009069	chr3:163787128-164323219	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv877836	chr3:163795964-164109377	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv877839	chr3:163823186-164126802	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv592435	chr3:163832166-164138131	Strong transcription Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv877840	chr3:163832988-164200220	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv877843	chr3:163835270-164126802	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
10	nsv877847	chr3:163849580-164126802	ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
11	nsv877849	chr3:163857437-164092986	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
12	nsv877852	chr3:163861355-164126802	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
13	nsv877858	chr3:163864862-164126802	Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
14	nsv592437	chr3:163885473-164095655	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
15	nsv877865	chr3:163902187-164126802	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv877867	chr3:163914791-164088664	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv877881	chr3:163922738-164076198	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv877886	chr3:163941553-164126802	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv877887	chr3:163941553-164138131	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv592440	chr3:163951886-164114553	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv1010490	chr3:163961100-164399225	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv1004944	chr3:163968837-164110498	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv536790	chr3:163968837-164110498	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv497973	chr3:163970658-164370204	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv1003471	chr3:163976235-164094643	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv1008208	chr3:163978650-164088858	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv877890	chr3:163989075-164114553	Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
28	nsv877891	chr3:163989075-164126802	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
29	nsv877892	chr3:163989075-164167085	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
30	nsv1007325	chr3:163998269-164094643	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
31	nsv1014815	chr3:164007081-164359622	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
32	nsv877893	chr3:164018044-164202045	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
33	esv1843213	chr3:164018044-164209573	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
34	nsv1006002	chr3:164021906-164653572	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
35	nsv877894	chr3:164026338-164109377	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
36	nsv877895	chr3:164046501-164126802	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
37	nsv877896	chr3:164046501-164138131	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
38	esv1803905	chr3:164047951-164062597	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
39	nsv998340	chr3:164047951-164325380	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:164048800-164051600	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr3:164049000-164051000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr3:164049000-164051600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:164049400-164051600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:164049600-164051600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr3:164049600-164051600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:164049600-164051600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:164049800-164051400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:164050000-164051400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:164050000-164051600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:164050200-164051000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:164050200-164051200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:164050200-164051600	Enhancers	Fetal Stomach	stomach
14	chr3:164050200-164052200	Enhancers	Fetal Intestine Small	intestine
15	chr3:164050400-164051400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr3:164050400-164051400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr3:164050400-164051600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:164050400-164051600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:164050400-164051600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:164050400-164051600	Enhancers	Ovary	ovary
21	chr3:164050400-164051600	Enhancers	Rectal Smooth Muscle	rectum
22	chr3:164050600-164051200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr3:164050600-164051200	Enhancers	Colon Smooth Muscle	Colon
24	chr3:164050600-164051400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:164050800-164051000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:164050800-164051000	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:164050800-164051600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr3:164050800-164051600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr3:164050800-164051600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:164050800-164059800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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