Variant report

Variant	rs12622683
Chromosome Location	chr2:113489255-113489256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113488382..113489971-chr2:113681773..113683855,2	MCF-7	breast:
2	chr2:113299836..113301714-chr2:113487045..113489440,2	MCF-7	breast:
3	chr2:113484246..113487026-chr2:113487818..113491393,4	MCF-7	breast:
4	chr2:113402071..113405083-chr2:113489239..113491182,3	K562	blood:
5	chr2:113402130..113405083-chr2:113489239..113490836,2	K562	blood:
6	chr2:113340842..113343108-chr2:113489160..113490667,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237753	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10165537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10187872	0.86[CHB][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs10193063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10200192	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10203064	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10496444	0.81[CHB][hapmap]
rs10496445	0.81[CHB][hapmap]
rs11123148	0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs11123149	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12463996	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12475027	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12478842	0.81[CHB][hapmap]
rs12711741	0.81[CHB][hapmap]
rs13009294	0.81[CHB][hapmap]
rs13013602	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13015273	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13016817	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13019249	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13026263	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13027814	0.81[CHB][hapmap]
rs13036237	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13382217	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13429613	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1609682	0.81[CHB][hapmap]
rs17649681	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071373	0.81[CHB][hapmap]
rs2138606	0.81[CHB][hapmap]
rs2862226	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3783521	0.81[CHB][hapmap]
rs3783525	0.81[CHB][hapmap]
rs3783526	0.81[CHB][hapmap]
rs3783546	0.81[CHB][hapmap]
rs3783550	0.81[CHB][hapmap]
rs3811040	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3827761	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4261731	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4848298	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4848301	0.80[CHB][hapmap]
rs4848302	0.81[CHB][hapmap]
rs4849115	0.81[CHB][hapmap]
rs4849118	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55762606	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58694576	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6542095	0.81[CHB][hapmap]
rs6706663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6712572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6721044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6721292	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6753803	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7577241	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7591704	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7594852	0.95[EUR][1000 genomes]
rs7599690	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7607470	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs908551	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]

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	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv526301	chr2:113451498-113495785	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12622683	ZC3H6	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113484200-113497200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:113484400-113494200	Weak transcription	A549	lung
3	chr2:113484400-113494800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr2:113484400-113495000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:113484400-113495600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:113484400-113495600	Weak transcription	Thymus	Thymus
7	chr2:113484400-113495800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:113484400-113495800	Weak transcription	GM12878-XiMat	blood
9	chr2:113484400-113496400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:113484400-113507400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:113484600-113494200	Weak transcription	Fetal Thymus	thymus
12	chr2:113484600-113507600	Weak transcription	Colonic Mucosa	Colon
13	chr2:113484800-113490000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:113484800-113490400	Weak transcription	Fetal Brain Male	brain
15	chr2:113484800-113490400	Weak transcription	Fetal Intestine Large	intestine
16	chr2:113484800-113494400	Weak transcription	NHEK	skin
17	chr2:113484800-113494600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:113484800-113494800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:113484800-113495600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:113484800-113496200	Weak transcription	NHDF-Ad	bronchial
21	chr2:113484800-113507600	Weak transcription	Primary B cells from cord blood	blood
22	chr2:113485000-113494800	Weak transcription	Dnd41	blood
23	chr2:113485200-113494800	Weak transcription	HMEC	breast
24	chr2:113486000-113491000	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:113486200-113494400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:113486200-113494600	Weak transcription	Fetal Stomach	stomach
27	chr2:113486200-113495000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:113486400-113490600	Weak transcription	Fetal Lung	lung
29	chr2:113486400-113491200	Weak transcription	Fetal Heart	heart
30	chr2:113486400-113495800	Weak transcription	HUVEC	blood vessel
31	chr2:113486600-113496200	Weak transcription	Placenta	Placenta
32	chr2:113486600-113511600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:113487400-113491200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:113487600-113495800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:113487600-113495800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:113487600-113496000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:113488200-113489400	Enhancers	K562	blood
38	chr2:113488200-113494200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:113488200-113494800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr2:113488200-113495800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr2:113488200-113495800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:113488200-113507400	Weak transcription	Spleen	Spleen
43	chr2:113488600-113495200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:113489200-113489400	Enhancers	Fetal Kidney	kidney

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