Variant report

Variant	rs9829540
Chromosome Location	chr3:113292302-113292303
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113286843..113290980-chr3:113291829..113295911,3	MCF-7	breast:
2	chr3:113213756..113215822-chr3:113289553..113292461,2	MCF-7	breast:
3	chr3:113233838..113235537-chr3:113290366..113293108,2	MCF-7	breast:
4	chr3:113282001..113285140-chr3:113291116..113294259,3	MCF-7	breast:
5	chr3:113255479..113257410-chr3:113291242..113292943,2	MCF-7	breast:
6	chr3:63897587..63899490-chr3:113291068..113293558,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163611	Chromatin interaction
ENSG00000163635	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs28539944	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28614095	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs58038438	1.00[ASN][1000 genomes]
rs60211993	1.00[ASN][1000 genomes]
rs61001715	1.00[ASN][1000 genomes]
rs61734094	1.00[ASN][1000 genomes]
rs6797630	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72950893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72950895	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73853723	1.00[ASN][1000 genomes]
rs73853724	1.00[ASN][1000 genomes]
rs73853725	1.00[ASN][1000 genomes]
rs73853728	1.00[ASN][1000 genomes]
rs73853729	1.00[ASN][1000 genomes]
rs73853730	1.00[ASN][1000 genomes]
rs73853731	1.00[ASN][1000 genomes]
rs73853734	1.00[ASN][1000 genomes]
rs73854364	1.00[ASN][1000 genomes]
rs73854366	1.00[ASN][1000 genomes]
rs73854516	1.00[ASN][1000 genomes]
rs73854517	1.00[ASN][1000 genomes]
rs73854518	1.00[ASN][1000 genomes]
rs73855948	1.00[ASN][1000 genomes]
rs73855949	1.00[ASN][1000 genomes]
rs9810754	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9827490	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9827772	0.83[YRI][hapmap];0.87[AMR][1000 genomes]
rs9846529	0.80[EUR][1000 genomes]
rs9860473	0.87[AMR][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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113276800-113294200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:113279200-113300000	Weak transcription	Thymus	Thymus
3	chr3:113280200-113299200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:113280200-113321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:113280400-113304000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:113280600-113302400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:113280600-113314800	Weak transcription	Spleen	Spleen
8	chr3:113281400-113302200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:113281600-113296400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:113281800-113296200	Strong transcription	Primary T cells from cord blood	blood
11	chr3:113283200-113296200	Strong transcription	GM12878-XiMat	blood
12	chr3:113285200-113329800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:113285200-113343400	Weak transcription	Small Intestine	intestine
14	chr3:113285400-113294200	Weak transcription	Esophagus	oesophagus
15	chr3:113285600-113292400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:113286000-113316800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:113287200-113301400	Weak transcription	Fetal Thymus	thymus
18	chr3:113287400-113293000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:113287800-113298600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:113287800-113299200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:113288000-113300000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:113288000-113302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:113289600-113293800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:113289600-113294200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:113289800-113299400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:113290000-113296400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:113290000-113296400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:113291000-113292600	Enhancers	A549	lung
29	chr3:113291400-113293800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:113291800-113296200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:113292000-113293800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr3:113292000-113294600	Enhancers	Fetal Intestine Large	intestine
33	chr3:113292200-113292600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr3:113292200-113292800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:113292200-113292800	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr3:113292200-113293800	Enhancers	Stomach Mucosa	stomach
37	chr3:113292200-113297800	Weak transcription	Primary B cells from cord blood	blood

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