Variant report

Variant	rs2540941
Chromosome Location	chr2:37065004-37065005
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	chr2:37053268..37055932-chr2:37062190..37065035,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1008838	0.86[CHB][hapmap]
rs1015600	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10182741	1.00[CHB][hapmap]
rs10188370	0.83[AMR][1000 genomes]
rs10189328	1.00[CHB][hapmap]
rs10201963	1.00[CHB][hapmap]
rs1043290	0.94[ASN][1000 genomes]
rs10490659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10495868	1.00[CHB][hapmap]
rs10865120	0.86[CHB][hapmap]
rs11124549	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11124552	1.00[CHB][hapmap]
rs11674211	1.00[CHB][hapmap]
rs11675109	1.00[CHB][hapmap]
rs11676225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11678303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs11682966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11686605	0.85[EUR][1000 genomes]
rs11691236	0.85[EUR][1000 genomes]
rs11904023	1.00[CHB][hapmap]
rs12479195	1.00[CHB][hapmap]
rs12624290	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13020894	0.80[ASN][1000 genomes]
rs13027958	0.80[ASN][1000 genomes]
rs13401327	1.00[CHB][hapmap]
rs13413438	1.00[CHB][hapmap]
rs17020005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17020024	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17020069	1.00[CHB][hapmap]
rs17020072	1.00[CHB][hapmap]
rs17020074	1.00[CHB][hapmap]
rs17020084	1.00[CHB][hapmap]
rs17442690	0.94[ASN][1000 genomes]
rs17442739	0.94[ASN][1000 genomes]
rs1861433	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs1861434	0.91[ASN][1000 genomes]
rs1861436	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2160379	0.84[ASN][1000 genomes]
rs2216106	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2255330	0.92[ASN][1000 genomes]
rs2287087	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2372812	0.94[ASN][1000 genomes]
rs2540918	0.81[ASN][1000 genomes]
rs2540919	0.86[CHB][hapmap]
rs2540920	0.81[ASN][1000 genomes]
rs2540925	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2540931	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2540936	0.85[ASN][1000 genomes]
rs2540939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2540940	0.98[ASN][1000 genomes]
rs2541000	0.86[CHB][hapmap]
rs2691104	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2691109	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2691110	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2691114	1.00[CHB][hapmap]
rs2691115	1.00[CHB][hapmap]
rs2691116	1.00[CHB][hapmap]
rs2691118	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2691122	0.81[ASN][1000 genomes]
rs2717492	0.81[ASN][1000 genomes]
rs2717494	1.00[CHB][hapmap]
rs2717495	0.89[ASN][1000 genomes]
rs2717496	0.84[ASN][1000 genomes]
rs2717501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2717505	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2717508	0.92[ASN][1000 genomes]
rs2717509	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2717510	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs2717511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2717512	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs2717518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2717522	1.00[CHB][hapmap]
rs28718824	1.00[CHB][hapmap]
rs2888418	0.96[ASN][1000 genomes]
rs3770775	1.00[CHB][hapmap]
rs3845779	1.00[CHB][hapmap]
rs41486347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4635515	1.00[CHB][hapmap]
rs55993128	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56186144	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57671539	0.90[EUR][1000 genomes]
rs57884362	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58970461	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59854977	0.85[EUR][1000 genomes]
rs6715033	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6739553	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6756876	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs723673	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs73924952	0.85[EUR][1000 genomes]
rs7562109	0.85[CHB][hapmap]
rs7581702	1.00[CHB][hapmap]
rs9789527	0.98[ASN][1000 genomes]
rs9789649	0.96[ASN][1000 genomes]
rs998321	1.00[CHB][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1011014	chr2:37027819-37095895	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv999465	chr2:37029347-37095895	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37060800-37070000	Weak transcription	HSMM	muscle
2	chr2:37061400-37067200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:37061400-37067400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:37062400-37074000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:37062400-37075800	Weak transcription	Brain Germinal Matrix	brain
6	chr2:37062600-37069400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:37062800-37073800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:37062800-37076000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:37062800-37095600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:37063000-37067000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:37063000-37067200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:37063000-37069600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:37063000-37071000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:37063000-37071200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:37063000-37074000	Weak transcription	Dnd41	blood
16	chr2:37063000-37074200	Weak transcription	Primary T cells from cord blood	blood
17	chr2:37063000-37076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:37063000-37093600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:37063200-37074200	Weak transcription	HUVEC	blood vessel
20	chr2:37063400-37066600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:37063400-37067000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:37063400-37067200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:37063800-37069600	Weak transcription	NHEK	skin
24	chr2:37064000-37076000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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