Variant report

Variant	rs2634675
Chromosome Location	chr12:48740855-48740856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48740296..48746434-chr12:48748194..48754526,9	MCF-7	breast:
2	chr12:48739061..48741247-chr20:30192176..30195111,2	MCF-7	breast:
3	chr12:48739614..48741833-chr12:48742167..48745928,3	MCF-7	breast:
4	chr12:48727374..48736715-chr12:48738720..48747602,13	K562	blood:

Variant related genes	Relation type
ENSG00000257735	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000257763	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000167528	Chromatin interaction
ENSG00000258273	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10431526	0.83[ASN][1000 genomes]
rs10467101	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10875750	0.87[JPT][hapmap]
rs10875767	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs10875770	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs10875772	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs10875792	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10875793	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10875799	0.95[ASN][1000 genomes]
rs11168433	0.87[JPT][hapmap]
rs11168450	0.87[JPT][hapmap]
rs11168459	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11168508	0.81[ASN][1000 genomes]
rs11168510	0.82[ASN][1000 genomes]
rs11168514	0.83[ASN][1000 genomes]
rs11168516	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11168520	0.92[ASN][1000 genomes]
rs11168536	0.95[ASN][1000 genomes]
rs12227601	0.81[ASN][1000 genomes]
rs12297470	0.86[JPT][hapmap]
rs12305511	0.87[JPT][hapmap]
rs12310813	0.87[JPT][hapmap]
rs12312134	0.81[JPT][hapmap]
rs12313745	0.91[ASN][1000 genomes]
rs12322347	0.91[ASN][1000 genomes]
rs12322348	0.91[ASN][1000 genomes]
rs1471997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17122812	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2012773	0.87[JPT][hapmap]
rs2054903	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2054904	0.93[ASN][1000 genomes]
rs2279464	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2450992	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2732439	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3185921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3751273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[ASN][1000 genomes]
rs4760622	0.87[JPT][hapmap]
rs4760625	0.81[ASN][1000 genomes]
rs4760687	0.87[JPT][hapmap]
rs4760695	0.87[JPT][hapmap]
rs4760696	0.87[JPT][hapmap]
rs4760697	0.87[JPT][hapmap]
rs6580659	0.85[JPT][hapmap]
rs7135779	0.86[JPT][hapmap]
rs7297298	0.81[ASN][1000 genomes]
rs7486424	0.87[JPT][hapmap]
rs8804	0.87[JPT][hapmap]
rs9634261	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
7	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
8	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv437752	chr12:48721832-48741219	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv1045159	chr12:48730024-48748940	Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2634675	ZNF641	cis	Muscle Skeletal	GTEx
rs2634675	H1FNT	cis	Muscle Skeletal	GTEx
rs2634675	ZNF641	cis	Thyroid	GTEx
rs2634675	ZNF641	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48729200-48743400	Weak transcription	Stomach Mucosa	stomach
2	chr12:48731200-48743800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48732400-48742600	Strong transcription	Left Ventricle	heart
4	chr12:48732600-48742600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:48733200-48742000	Strong transcription	Brain Hippocampus Middle	brain
6	chr12:48733200-48742200	Strong transcription	Fetal Thymus	thymus
7	chr12:48733400-48741000	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:48733600-48742000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr12:48733600-48742200	Strong transcription	Primary B cells from cord blood	blood
10	chr12:48733600-48743800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:48733800-48742000	Strong transcription	Liver	Liver
12	chr12:48733800-48742200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48733800-48742800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:48734000-48741800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:48734000-48741800	Strong transcription	Fetal Brain Female	brain
16	chr12:48734000-48742000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:48734000-48742200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:48734000-48742600	Strong transcription	Fetal Muscle Leg	muscle
19	chr12:48734200-48742000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:48734600-48741800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:48734600-48742000	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr12:48734800-48741600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr12:48735000-48743000	Weak transcription	Fetal Heart	heart
24	chr12:48735200-48743600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:48735400-48742000	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:48735400-48742000	Strong transcription	Stomach Smooth Muscle	stomach
27	chr12:48735400-48742200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:48735400-48742600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:48735400-48743200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:48735600-48741400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:48735600-48741800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:48735600-48742000	Strong transcription	Brain Germinal Matrix	brain
33	chr12:48735600-48742000	Strong transcription	Fetal Intestine Large	intestine
34	chr12:48735600-48742000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr12:48735800-48741600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:48735800-48741800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:48735800-48741800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:48735800-48741800	Strong transcription	Adipose Nuclei	Adipose
39	chr12:48735800-48742000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:48735800-48742200	Strong transcription	Brain Anterior Caudate	brain
41	chr12:48735800-48742400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:48736000-48741600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:48736000-48741600	Strong transcription	Brain Angular Gyrus	brain
44	chr12:48736000-48741800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:48736000-48741800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:48736000-48741800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:48736000-48741800	Strong transcription	Brain Substantia Nigra	brain
48	chr12:48736000-48741800	Strong transcription	Fetal Lung	lung
49	chr12:48736000-48741800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:48736000-48742000	Strong transcription	Colon Smooth Muscle	Colon

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