Variant report

Variant	rs10258841
Chromosome Location	chr7:104976859-104976860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:104970519..104973414-chr7:104974940..104976942,3	MCF-7	breast:
2	chr7:104781272..104782333-chr7:104976099..104977101,5	MCF-7	breast:
3	chr7:104793089..104794036-chr7:104976109..104977046,2	MCF-7	breast:
4	chr7:104966725..104970068-chr7:104975373..104978585,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201179	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10224564	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10228503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10230128	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10230449	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10233695	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10235252	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10240574	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10248422	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10248954	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10249170	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10252295	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10253496	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10255779	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10259721	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10261613	0.84[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10261738	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10261782	0.96[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10267633	1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10269027	0.87[TSI][hapmap]
rs10272634	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10276153	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10280336	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10280470	0.88[GIH][hapmap];0.87[TSI][hapmap]
rs10953473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11764361	0.82[ASN][1000 genomes]
rs11769318	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11769936	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11973742	0.86[EUR][1000 genomes]
rs11973780	0.87[EUR][1000 genomes]
rs12537761	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12666949	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12669532	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12705305	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13223001	0.96[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13237370	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13246886	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17721991	0.88[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17778396	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1859786	0.83[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap]
rs1917047	0.96[GIH][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978201	0.96[GIH][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2040913	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2214928	0.80[MKK][hapmap];0.87[TSI][hapmap]
rs2237606	0.83[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap]
rs2237610	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs2237611	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2237615	0.96[GIH][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237616	0.96[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237618	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2237619	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2237620	0.96[GIH][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2240465	0.92[GIH][hapmap]
rs2286124	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299312	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2299313	0.96[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299314	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299316	0.87[EUR][1000 genomes]
rs2299320	0.96[GIH][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2299325	0.86[ASN][1000 genomes]
rs2299326	0.96[GIH][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2385542	0.84[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2385556	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28461911	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28823350	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34003298	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34154773	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34717863	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34789097	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35442357	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35973577	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35993922	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3735372	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3779208	0.96[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3779209	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3801283	0.96[GIH][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4610671	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4727622	0.92[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4730078	0.96[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55796396	0.85[EUR][1000 genomes]
rs60446665	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62488069	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6466045	0.87[TSI][hapmap]
rs6971241	0.83[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs717352	0.96[GIH][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs725506	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73186027	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73188303	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73188305	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73188321	0.83[ASN][1000 genomes]
rs7780887	0.87[TSI][hapmap]
rs7808168	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8180735	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8180737	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9641343	0.84[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9641345	0.96[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs9641347	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9641348	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34588	chr7:104737612-105153242	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	17 gene(s)	inside rSNPs	diseases
2	esv2757233	chr7:104758250-105208492	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv2759549	chr7:104758250-105208492	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv8196	chr7:104763559-105155978	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv34580	chr7:104763580-105153242	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2758127	chr7:104766707-105110581	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1028228	chr7:104807207-105182998	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv932138	chr7:104826194-105152816	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1015688	chr7:104849770-105182998	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv1029832	chr7:104905057-105112489	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv1023767	chr7:104931143-105190662	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv539049	chr7:104931143-105190662	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1034689	chr7:104950564-105085879	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104948600-104988000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:104957400-104986800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:104958000-104983200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:104961600-104980200	Weak transcription	Psoas Muscle	Psoas
5	chr7:104962800-104992600	Weak transcription	Fetal Intestine Small	intestine
6	chr7:104963000-104983000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr7:104963200-104991200	Weak transcription	Fetal Stomach	stomach
8	chr7:104963600-104980000	Weak transcription	Brain Anterior Caudate	brain
9	chr7:104964200-104977200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr7:104964200-104983200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr7:104964400-104983400	Weak transcription	Primary T cells from cord blood	blood
12	chr7:104966200-104980600	Weak transcription	Primary B cells from cord blood	blood
13	chr7:104966200-104985800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:104967200-104986200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:104968200-104986800	Weak transcription	Gastric	stomach
16	chr7:104970000-104979800	Weak transcription	Brain Angular Gyrus	brain
17	chr7:104970800-104977800	Enhancers	Dnd41	blood
18	chr7:104972200-104983200	Weak transcription	A549	lung
19	chr7:104972400-104983200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:104973000-104980000	Weak transcription	Right Ventricle	heart
21	chr7:104973200-104980000	Weak transcription	Ovary	ovary
22	chr7:104973200-104983200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr7:104973200-104998800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:104973400-104980000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:104973600-104980000	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:104973600-104980800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:104973600-104981000	Weak transcription	K562	blood
28	chr7:104973600-104981600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:104973800-104980200	Weak transcription	Lung	lung
30	chr7:104973800-104985400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:104976200-104980400	Weak transcription	NHLF	lung
32	chr7:104976800-104991600	Weak transcription	HSMM	muscle

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