Variant report

Variant	rs7609124
Chromosome Location	chr2:48337354-48337355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48334851..48336463-chr2:48336834..48339382,2	K562	blood:
2	chr2:48336673..48339163-chr2:48642028..48644836,2	K562	blood:
3	chr2:48009304..48010827-chr2:48336358..48338328,2	K562	blood:
4	chr2:48336922..48340984-chr2:48645140..48651052,10	MCF-7	breast:
5	chr2:48336515..48341862-chr2:48539044..48543633,11	MCF-7	breast:
6	chr2:48131582..48133722-chr2:48336786..48340166,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116062	Chromatin interaction
ENSG00000170802	Chromatin interaction
ENSG00000233230	Chromatin interaction
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10167776	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11125157	0.82[AMR][1000 genomes]
rs11125165	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11125166	0.81[ASN][1000 genomes]
rs1473611	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1483210	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1483215	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17324704	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1825320	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1878079	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1878081	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2128716	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2128719	0.83[ASN][1000 genomes]
rs2136456	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2348717	1.00[ASN][1000 genomes]
rs2348718	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28460586	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2882003	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4146603	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952904	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4952905	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953534	0.81[AMR][1000 genomes]
rs4953544	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4953546	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4953548	1.00[ASN][1000 genomes]
rs4953549	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953552	0.89[ASN][1000 genomes]
rs4953553	0.89[ASN][1000 genomes]
rs4953555	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953556	0.89[ASN][1000 genomes]
rs4953557	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58178746	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58525908	0.89[ASN][1000 genomes]
rs6545017	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6545019	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6545021	1.00[ASN][1000 genomes]
rs6545023	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6706664	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6712238	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718037	1.00[ASN][1000 genomes]
rs6722407	1.00[ASN][1000 genomes]
rs6723952	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750246	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6759902	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7563749	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7570354	0.89[ASN][1000 genomes]
rs7589460	1.00[ASN][1000 genomes]
rs7605361	1.00[ASN][1000 genomes]
rs7605366	0.90[ASN][1000 genomes]
rs900506	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs900510	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs900511	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs922902	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs922903	1.00[ASN][1000 genomes]
rs963133	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs963135	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9677729	0.89[ASN][1000 genomes]
rs968888	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs973894	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs990063	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs990549	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs999036	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription 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	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1000455	chr2:48202161-48362638	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv581773	chr2:48277490-48443109	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48333200-48338200	Enhancers	HMEC	breast
2	chr2:48333600-48338200	Weak transcription	Gastric	stomach
3	chr2:48333800-48338200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:48333800-48338200	Weak transcription	Stomach Mucosa	stomach
5	chr2:48333800-48338400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:48333800-48338400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:48333800-48338400	Weak transcription	Ovary	ovary
8	chr2:48334000-48338200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:48334000-48338200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:48334000-48338200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:48334200-48337600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:48334200-48337800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:48334200-48338200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:48334200-48338200	Weak transcription	Primary B cells from cord blood	blood
15	chr2:48334200-48338200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:48334200-48338200	Weak transcription	Primary T cells from cord blood	blood
17	chr2:48334200-48338200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:48334200-48338200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:48334200-48338200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:48334200-48338200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:48334400-48337800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:48334400-48337800	Weak transcription	Brain Substantia Nigra	brain
23	chr2:48334400-48338000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:48334400-48338000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:48334400-48338000	Weak transcription	Brain Germinal Matrix	brain
26	chr2:48334400-48338000	Weak transcription	Fetal Brain Female	brain
27	chr2:48334400-48338000	Weak transcription	Fetal Kidney	kidney
28	chr2:48334400-48338000	Weak transcription	Dnd41	blood
29	chr2:48334400-48338200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:48334400-48338200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:48334400-48338200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:48334400-48338200	Weak transcription	Colonic Mucosa	Colon
33	chr2:48334400-48338200	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:48334400-48338200	Weak transcription	Fetal Stomach	stomach
35	chr2:48334400-48338200	Weak transcription	Fetal Thymus	thymus
36	chr2:48334400-48338200	Weak transcription	Pancreas	Pancrea
37	chr2:48334400-48338200	Weak transcription	Psoas Muscle	Psoas
38	chr2:48334400-48338200	Weak transcription	GM12878-XiMat	blood
39	chr2:48334400-48338400	Weak transcription	Fetal Brain Male	brain
40	chr2:48334600-48337800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:48334600-48337800	Weak transcription	Brain Anterior Caudate	brain
42	chr2:48334600-48338000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:48334600-48338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:48334600-48338200	Weak transcription	Liver	Liver
45	chr2:48334600-48338200	Weak transcription	Brain Angular Gyrus	brain
46	chr2:48334600-48338200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:48334600-48338200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:48334800-48337800	Weak transcription	HSMMtube	muscle
49	chr2:48334800-48338000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:48334800-48338000	Weak transcription	Duodenum Mucosa	Duodenum

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