Variant report

Variant	rs12846
Chromosome Location	chr2:97477374-97477375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:97467639..97469941-chr2:97475793..97477509,2	MCF-7	breast:
2	chr2:97302214..97304255-chr2:97474518..97477547,4	K562	blood:

Variant related genes	Relation type
ENSG00000114982	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11897786	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317911	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1320149	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13419073	0.81[AMR][1000 genomes]
rs17119598	0.84[EUR][1000 genomes]
rs2276654	0.80[EUR][1000 genomes]
rs3731941	0.85[EUR][1000 genomes]
rs55674661	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58147284	0.81[AMR][1000 genomes]
rs62152788	0.85[EUR][1000 genomes]
rs62152790	0.87[EUR][1000 genomes]
rs62152793	0.84[EUR][1000 genomes]
rs62152794	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62152795	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6576989	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7580942	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7594727	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7608621	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh 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	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv834307	chr2:97321447-97479266	Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
10	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
12	nsv1009720	chr2:97464803-97522856	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv535830	chr2:97464803-97522856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12846	FAHD2CP	cis	Muscle Skeletal	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97440000-97480800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:97454600-97481000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:97454600-97481000	Weak transcription	NHEK	skin
4	chr2:97455200-97477600	Weak transcription	HSMMtube	muscle
5	chr2:97455400-97480600	Weak transcription	Hela-S3	cervix
6	chr2:97462000-97480800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:97464600-97477600	Weak transcription	Osteobl	bone
8	chr2:97464600-97480800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:97465200-97481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:97465400-97481200	Weak transcription	Small Intestine	intestine
11	chr2:97466000-97481200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:97466800-97478000	Weak transcription	NHLF	lung
13	chr2:97466800-97478600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:97466800-97480600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:97466800-97481000	Weak transcription	HMEC	breast
16	chr2:97467800-97481000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:97467800-97481000	Weak transcription	Fetal Brain Male	brain
18	chr2:97468000-97480800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:97468000-97480800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:97468000-97481000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:97468400-97480800	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:97472400-97478400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:97472800-97477600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:97472800-97477600	Strong transcription	Fetal Stomach	stomach
25	chr2:97472800-97478000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr2:97472800-97478400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:97473000-97479600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr2:97473000-97481000	Weak transcription	Primary B cells from cord blood	blood
29	chr2:97473200-97480800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:97473200-97480800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:97473600-97481000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:97473800-97481000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:97474000-97480800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:97474200-97477400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:97474200-97477400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:97474200-97477400	Strong transcription	Rectal Smooth Muscle	rectum
37	chr2:97474200-97478600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:97474200-97479400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:97474200-97479400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:97474200-97480800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr2:97474200-97480800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:97474200-97480800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:97474200-97481000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:97474400-97477400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:97474400-97479200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:97474400-97480800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:97474600-97477400	Strong transcription	Fetal Brain Female	brain
48	chr2:97474600-97481000	Weak transcription	Ovary	ovary
49	chr2:97474800-97478000	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr2:97475000-97478200	Strong transcription	GM12878-XiMat	blood

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