Variant report

Variant	rs2258342
Chromosome Location	chr12:48690363-48690364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48688262..48692290-chr12:48702214..48707293,5	K562	blood:
2	chr12:48593487..48595723-chr12:48689162..48691231,3	K562	blood:
3	chr12:48689964..48692021-chr12:48694764..48697453,3	MCF-7	breast:
4	chr12:48682061..48686479-chr12:48688143..48691883,6	K562	blood:
5	chr12:48689650..48692193-chr12:48742789..48745705,2	K562	blood:
6	chr12:48680562..48682797-chr12:48688715..48691085,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257735	Chromatin interaction
ENSG00000167528	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10492080	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap]
rs1074174	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783231	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs10783232	0.93[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs10783237	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10783239	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168451	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11168455	0.93[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs11609399	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12822085	0.85[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs1387256	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1476608	0.87[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs1489111	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1552551	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17122651	0.87[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs1906718	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2013956	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2054902	0.84[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2130095	0.88[ASN][1000 genomes]
rs2130096	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2468947	0.84[ASN][1000 genomes]
rs2468948	0.80[ASN][1000 genomes]
rs2468950	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634669	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2634679	0.87[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2634699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2634701	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2732440	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2732443	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2732446	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2732451	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2732455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2732458	0.87[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2732460	0.88[EUR][1000 genomes]
rs2732464	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2732474	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2732475	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2732476	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2732477	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2732478	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2732487	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932090	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2932106	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2932107	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2956704	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3989427	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4075913	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4141065	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4760620	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap]
rs4760623	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760683	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs4760685	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4760692	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4760698	0.93[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs60908321	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6580656	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs6580660	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7134201	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7134565	0.88[ASN][1000 genomes]
rs726354	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap]
rs7294641	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7304709	0.93[ASN][1000 genomes]
rs7305418	0.92[CEU][hapmap]
rs7315258	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs7485057	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs757556	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7953726	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7969749	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs879242	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs901962	0.87[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs901963	0.87[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs901964	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9645811	0.96[ASN][1000 genomes]
rs987986	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv899062	chr12:48658212-48711867	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv899063	chr12:48664989-48713768	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv899064	chr12:48664989-48721832	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv899065	chr12:48667019-48711867	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv899066	chr12:48667019-48713768	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	esv34952	chr12:48672333-48703533	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv469369	chr12:48675783-48711867	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv469370	chr12:48675783-48711867	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv469372	chr12:48675783-48711867	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv470290	chr12:48675783-48711867	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv558791	chr12:48675783-48711867	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2258342	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48686000-48690800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48688400-48690600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:48689800-48690400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
4	chr12:48689800-48690400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:48689800-48690400	Enhancers	Right Ventricle	heart
6	chr12:48689800-48690600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:48689800-48691000	Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr12:48690000-48691200	Active TSS	Brain Hippocampus Middle	brain
9	chr12:48690000-48691200	Flanking Active TSS	K562	blood
10	chr12:48690200-48690400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr12:48690200-48690400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:48690200-48690400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:48690200-48690400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:48690200-48690400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr12:48690200-48690400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr12:48690200-48690400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:48690200-48690400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:48690200-48690400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr12:48690200-48690400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:48690200-48690400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:48690200-48690400	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr12:48690200-48690400	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr12:48690200-48690400	Enhancers	Fetal Intestine Large	intestine
24	chr12:48690200-48690400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr12:48690200-48690400	Enhancers	Placenta	Placenta
26	chr12:48690200-48690400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr12:48690200-48690400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr12:48690200-48690400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr12:48690200-48690400	Active TSS	HUVEC	blood vessel
30	chr12:48690200-48690400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr12:48690200-48690400	Flanking Active TSS	NH-A	brain
32	chr12:48690200-48690400	Flanking Active TSS	NHDF-Ad	bronchial
33	chr12:48690200-48690400	Flanking Active TSS	Osteobl	bone
34	chr12:48690200-48690600	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr12:48690200-48690600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:48690200-48690600	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr12:48690200-48690600	Active TSS	Right Atrium	heart
38	chr12:48690200-48690600	Enhancers	Stomach Mucosa	stomach
39	chr12:48690200-48690800	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr12:48690200-48690800	Flanking Active TSS	Thymus	Thymus
41	chr12:48690200-48691000	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr12:48690200-48691000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr12:48690200-48691000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:48690200-48691000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr12:48690200-48691000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr12:48690200-48691000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:48690200-48691000	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr12:48690200-48691000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
49	chr12:48690200-48691000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:48690200-48691000	Active TSS	Fetal Heart	heart

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