Variant report

Variant	rs16861230
Chromosome Location	chr3:113326429-113326430
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	chr3:113318238..113321101-chr3:113324949..113327480,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072858	Chromatin interaction

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

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

rs_ID	r²[population]
rs10934239	0.81[AMR][1000 genomes]
rs10934240	0.81[AMR][1000 genomes]
rs11914863	0.86[AMR][1000 genomes]
rs11918910	0.86[AMR][1000 genomes]
rs11920913	0.81[AMR][1000 genomes]
rs11921407	0.86[AMR][1000 genomes]
rs12486414	0.93[AMR][1000 genomes]
rs12489192	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12490048	1.00[AMR][1000 genomes]
rs12490651	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12491540	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12492290	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12492542	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12492783	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12493602	0.93[AMR][1000 genomes]
rs12493935	0.81[AMR][1000 genomes]
rs12494777	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12495298	0.86[AMR][1000 genomes]
rs12495713	0.93[AMR][1000 genomes]
rs12496604	0.93[AMR][1000 genomes]
rs12496617	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12497754	0.93[AMR][1000 genomes]
rs16861233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16861235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16861331	0.93[AMR][1000 genomes]
rs2292512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2566972	0.81[AMR][1000 genomes]
rs2603791	0.81[AMR][1000 genomes]
rs3773686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57010522	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113285200-113329800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:113285200-113343400	Weak transcription	Small Intestine	intestine
3	chr3:113317200-113330800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:113320400-113333200	Weak transcription	Fetal Intestine Large	intestine
5	chr3:113320400-113345600	Weak transcription	Fetal Intestine Small	intestine
6	chr3:113320800-113347600	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr3:113321200-113331600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:113321200-113333000	Weak transcription	Spleen	Spleen
9	chr3:113321200-113349200	Weak transcription	Brain Angular Gyrus	brain
10	chr3:113321200-113349600	Weak transcription	Lung	lung
11	chr3:113322600-113348600	Weak transcription	Colonic Mucosa	Colon
12	chr3:113323200-113342400	Weak transcription	Pancreas	Pancrea
13	chr3:113324200-113326800	Genic enhancers	GM12878-XiMat	blood
14	chr3:113324400-113326600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:113324400-113326800	Genic enhancers	Primary T cells from cord blood	blood
16	chr3:113324400-113328000	Enhancers	Fetal Thymus	thymus
17	chr3:113324600-113326600	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr3:113324600-113326800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:113324600-113327200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr3:113325000-113326600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:113325000-113326800	Enhancers	H9 Cell Line	embryonic stem cell
22	chr3:113325000-113326800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr3:113325200-113326600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:113325200-113326600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:113325200-113326800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:113325200-113326800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:113325400-113326600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr3:113325400-113326600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:113325400-113326600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:113325800-113326600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:113325800-113326800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr3:113326000-113326600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr3:113326000-113334000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:113326000-113334600	Weak transcription	Fetal Lung	lung
35	chr3:113326200-113326600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr3:113326200-113326600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr3:113326200-113326600	Enhancers	Psoas Muscle	Psoas
38	chr3:113326200-113326800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:113326200-113327000	Genic enhancers	Primary B cells from cord blood	blood
40	chr3:113326200-113327200	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr3:113326200-113327800	Genic enhancers	Thymus	Thymus
42	chr3:113326200-113329800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:113326200-113335600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:113326200-113340000	Weak transcription	Fetal Stomach	stomach
45	chr3:113326200-113340600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr3:113326400-113326600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr3:113326400-113326600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:113326400-113326600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:113326400-113326800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:113326400-113327000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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