Variant report

Variant	rs34556232
Chromosome Location	chr2:58465927-58465928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr2:58465922-58465975	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:58463999..58466723-chr2:58466859..58468849,2	K562	blood:
2	chr2:58448319..58453371-chr2:58460380..58466527,5	K562	blood:
3	chr2:58465119..58467411-chr2:58475928..58478281,2	K562	blood:
4	chr2:58269958..58272240-chr2:58464322..58467065,2	K562	blood:
5	chr2:58465064..58466723-chr2:58466859..58468445,2	K562	blood:
6	chr2:58272245..58275889-chr2:58464232..58469335,5	K562	blood:
7	chr2:58444316..58447844-chr2:58463533..58467170,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000273063	TF binding region
ENSG00000115392	Chromatin interaction
ENSG00000273063	Chromatin interaction
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10184957	0.91[EUR][1000 genomes]
rs11903212	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12616896	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12624152	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12713376	0.94[EUR][1000 genomes]
rs12988249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006005	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13023405	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13032851	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13410228	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13422760	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1404457	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1404459	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1404460	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34335951	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35341336	1.00[AFR][1000 genomes]
rs35773188	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35925771	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3755296	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3771222	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55809167	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57267169	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61746304	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6709533	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6714952	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6752935	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7558066	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7561771	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3345369	chr2:58465514-58466016	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58391000-58467000	Weak transcription	HMEC	breast
2	chr2:58416600-58467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:58432000-58466400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:58438600-58466400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:58439000-58467400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:58440000-58467400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr2:58440600-58467400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:58444200-58466200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:58450000-58466200	Weak transcription	HUVEC	blood vessel
10	chr2:58452000-58467400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:58452000-58467400	Weak transcription	NHLF	lung
12	chr2:58453800-58467400	Weak transcription	NHDF-Ad	bronchial
13	chr2:58454600-58466800	Weak transcription	HSMM	muscle
14	chr2:58454800-58466200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:58454800-58466400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:58454800-58467400	Weak transcription	Primary B cells from cord blood	blood
17	chr2:58454800-58467400	Weak transcription	Fetal Thymus	thymus
18	chr2:58454800-58467400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:58454800-58467400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:58454800-58467400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr2:58455000-58466200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:58455000-58466200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:58455000-58466200	Weak transcription	Fetal Intestine Small	intestine
24	chr2:58455000-58466800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:58455000-58466800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:58455000-58467400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:58455000-58467400	Weak transcription	Fetal Stomach	stomach
28	chr2:58455000-58467400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:58455000-58467600	Weak transcription	Left Ventricle	heart
30	chr2:58455000-58467600	Weak transcription	Ovary	ovary
31	chr2:58455000-58468000	Weak transcription	Gastric	stomach
32	chr2:58455000-58468000	Weak transcription	Spleen	Spleen
33	chr2:58455200-58467400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:58455200-58467400	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:58460800-58467400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:58461000-58466200	Weak transcription	Brain Germinal Matrix	brain
37	chr2:58461000-58467800	Weak transcription	Small Intestine	intestine
38	chr2:58461400-58466200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:58462000-58467200	Weak transcription	Osteobl	bone
40	chr2:58462400-58466200	Weak transcription	Liver	Liver
41	chr2:58462400-58467400	Weak transcription	Fetal Heart	heart
42	chr2:58462600-58466400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:58462600-58466400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr2:58462600-58466800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:58462600-58466800	Weak transcription	Brain Substantia Nigra	brain
46	chr2:58462600-58467400	Weak transcription	Pancreas	Pancrea
47	chr2:58463400-58466000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:58463600-58467400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:58464200-58467000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:58464800-58466000	Enhancers	Fetal Brain Female	brain

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