Variant report

Variant	rs9842559
Chromosome Location	chr3:113252705-113252706
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113225298..113228021-chr3:113252260..113254913,2	K562	blood:
2	chr3:113215914..113218639-chr3:113252642..113255587,3	MCF-7	breast:
3	chr3:113229615..113239929-chr3:113247196..113257849,45	MCF-7	breast:
4	chr20:61846286..61848363-chr3:113251582..113253331,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149658	Chromatin interaction
ENSG00000163611	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11537650	0.87[EUR][1000 genomes]
rs13082603	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs13092925	0.85[EUR][1000 genomes]
rs1463643	0.86[EUR][1000 genomes]
rs1471883	1.00[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1471884	1.00[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1552433	1.00[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16861103	0.95[CEU][hapmap]
rs2087130	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2399477	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2399480	0.87[EUR][1000 genomes]
rs2669909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4396864	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs60634072	0.80[EUR][1000 genomes]
rs6438160	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6769604	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6783387	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6793704	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72946748	0.81[EUR][1000 genomes]
rs7618226	0.86[EUR][1000 genomes]
rs7623919	1.00[CEU][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7628945	0.86[EUR][1000 genomes]
rs7631335	0.86[EUR][1000 genomes]
rs7635676	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637618	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7646188	1.00[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7650671	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846539	0.87[EUR][1000 genomes]
rs9852703	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9854686	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870996	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9874747	0.85[EUR][1000 genomes]
rs9877649	0.87[EUR][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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113250400-113252800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr3:113250400-113253200	Active TSS	Sigmoid Colon	Sigmoid Colon
3	chr3:113250600-113253200	Active TSS	Thymus	Thymus
4	chr3:113250600-113253400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:113250800-113253000	Active TSS	Duodenum Mucosa	Duodenum
6	chr3:113250800-113253000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
7	chr3:113250800-113253000	Bivalent/Poised TSS	A549	lung
8	chr3:113250800-113253200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:113250800-113253200	Active TSS	Rectal Smooth Muscle	rectum
10	chr3:113250800-113253200	Active TSS	Stomach Mucosa	stomach
11	chr3:113250800-113254600	Active TSS	GM12878-XiMat	blood
12	chr3:113251000-113252800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr3:113251000-113252800	Active TSS	Primary T cells fromperipheralblood	blood
14	chr3:113251000-113252800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:113251000-113252800	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr3:113251000-113252800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:113251000-113252800	Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr3:113251000-113252800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr3:113251000-113252800	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr3:113251000-113253200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr3:113251000-113253200	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr3:113251000-113253800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:113251200-113252800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:113251200-113252800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
25	chr3:113251200-113252800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr3:113251200-113252800	Active TSS	Primary T cells from cord blood	blood
27	chr3:113251200-113253400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:113251600-113252800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
29	chr3:113251600-113253800	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr3:113252000-113252800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
31	chr3:113252000-113253000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:113252000-113253200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr3:113252000-113253400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:113252000-113253400	Flanking Bivalent TSS/Enh	Dnd41	blood
35	chr3:113252200-113252800	Bivalent/Poised TSS	Fetal Kidney	kidney
36	chr3:113252200-113253600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
37	chr3:113252400-113252800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:113252400-113252800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:113252400-113252800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:113252400-113252800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
41	chr3:113252400-113252800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
42	chr3:113252400-113253400	Flanking Active TSS	Fetal Thymus	thymus
43	chr3:113252400-113253400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
44	chr3:113252400-113253600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
45	chr3:113252400-113254000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr3:113252400-113255000	Weak transcription	Gastric	stomach
47	chr3:113252600-113252800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
48	chr3:113252600-113252800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
49	chr3:113252600-113252800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:113252600-113252800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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