Variant report

Variant	rs2130096
Chromosome Location	chr12:48742489-48742490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48740296..48746434-chr12:48748194..48754526,9	MCF-7	breast:
2	chr12:48740907..48742946-chr12:48743021..48744777,2	K562	blood:
3	chr12:48741301..48746348-chr12:48747901..48753728,9	MCF-7	breast:
4	chr12:48737714..48740514-chr12:48742056..48744740,4	K562	blood:
5	chr12:48727374..48736715-chr12:48738720..48747602,13	K562	blood:
6	chr12:48590039..48593666-chr12:48742360..48744824,3	K562	blood:
7	chr12:48712249..48713811-chr12:48741088..48742691,2	K562	blood:
8	chr12:48729486..48731368-chr12:48741575..48744157,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257735	Chromatin interaction
ENSG00000257763	Chromatin interaction
ENSG00000269514	Chromatin interaction
ENSG00000167528	Chromatin interaction
ENSG00000258273	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1074174	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783239	0.85[EUR][1000 genomes]
rs1387256	0.82[EUR][1000 genomes]
rs1489111	0.80[ASN][1000 genomes]
rs1552551	0.85[EUR][1000 genomes]
rs1906718	0.81[ASN][1000 genomes]
rs2054902	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2258342	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2468947	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2468948	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2468950	0.95[EUR][1000 genomes]
rs2634669	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2634674	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2634679	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2634701	0.80[ASN][1000 genomes]
rs2732440	0.90[EUR][1000 genomes]
rs2732443	0.80[ASN][1000 genomes]
rs2732446	0.90[EUR][1000 genomes]
rs2732451	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2732455	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2732458	0.98[EUR][1000 genomes]
rs2732460	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2732464	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732474	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2732475	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2732476	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2732477	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2732478	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2732487	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2932090	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932107	0.80[ASN][1000 genomes]
rs2956704	0.81[ASN][1000 genomes]
rs4760623	0.84[EUR][1000 genomes]
rs60908321	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7134201	0.81[ASN][1000 genomes]
rs7953726	0.82[EUR][1000 genomes]
rs901962	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901964	0.80[ASN][1000 genomes]
rs987986	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2130096	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:120 , 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	chr12:48733600-48743800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:48733800-48742800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:48734000-48742600	Strong transcription	Fetal Muscle Leg	muscle
8	chr12:48735000-48743000	Weak transcription	Fetal Heart	heart
9	chr12:48735200-48743600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:48735400-48742600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:48735400-48743200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:48737400-48743400	Weak transcription	NHEK	skin
13	chr12:48737600-48743000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:48737600-48743400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:48737800-48743200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:48737800-48743200	Weak transcription	HepG2	liver
17	chr12:48737800-48743600	Weak transcription	HSMMtube	muscle
18	chr12:48738400-48743200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr12:48738600-48743800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:48739000-48743200	Weak transcription	Right Atrium	heart
21	chr12:48739000-48743600	Weak transcription	NH-A	brain
22	chr12:48739400-48743200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:48739600-48743200	Weak transcription	Fetal Brain Male	brain
24	chr12:48739600-48743200	Weak transcription	K562	blood
25	chr12:48739600-48743400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:48739600-48743400	Weak transcription	Small Intestine	intestine
27	chr12:48740600-48743200	Weak transcription	NHDF-Ad	bronchial
28	chr12:48741200-48743600	Weak transcription	NHLF	lung
29	chr12:48741400-48743000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:48741600-48742600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:48741600-48742800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:48741600-48742800	Weak transcription	Hela-S3	cervix
33	chr12:48741600-48743200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:48741600-48743200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:48741600-48743600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:48741600-48743600	Weak transcription	Brain Angular Gyrus	brain
37	chr12:48741600-48743800	Weak transcription	HSMM	muscle
38	chr12:48741800-48742600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr12:48741800-48742800	Weak transcription	Adipose Nuclei	Adipose
40	chr12:48741800-48743000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:48741800-48743000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:48741800-48743000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:48741800-48743000	Weak transcription	Fetal Lung	lung
44	chr12:48741800-48743000	Weak transcription	Osteobl	bone
45	chr12:48741800-48743200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:48741800-48743200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:48741800-48743200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:48741800-48743200	Weak transcription	Fetal Kidney	kidney
49	chr12:48741800-48743200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr12:48741800-48743200	Weak transcription	Rectal Smooth Muscle	rectum

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