Variant report

Variant	rs6546893
Chromosome Location	chr2:74432449-74432450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:74432148-74432524	PANC-1	pancreas:	n/a	n/a
2	WRNIP1	chr2:74432415-74432504	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:74432388-74433832	HepG2	liver:	n/a	n/a
4	TBL1XR1	chr2:74432352-74432473	K562	blood:	n/a	n/a
5	POLR2A	chr2:74432280-74432569	K562	blood:	n/a	n/a
6	POLR2A	chr2:74432432-74432617	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:74432297-74433208	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:74432209-74432874	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr2:74432278-74433850	A549	lung:	n/a	n/a
10	POLR2A	chr2:74432350-74432577	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:74432339-74432627	K562	blood:	n/a	n/a
12	POLR2A	chr2:74431026-74433991	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74210903..74212994-chr2:74431667..74434283,2	MCF-7	breast:
2	chr2:74405932..74407579-chr2:74429494..74432993,3	MCF-7	breast:
3	chr2:74431867..74433387-chr2:74475531..74477876,2	MCF-7	breast:

No data

Variant related genes	Relation type
MTHFD2	TF binding region
ENSG00000235499	Chromatin interaction
ENSG00000114978	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1095968	0.85[EUR][1000 genomes]
rs11126426	0.87[ASN][1000 genomes]
rs12196	0.82[EUR][1000 genomes]
rs13426653	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1620482	0.87[ASN][1000 genomes]
rs1667601	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1667609	0.88[ASN][1000 genomes]
rs1723281	0.87[EUR][1000 genomes]
rs1723285	0.85[EUR][1000 genomes]
rs3108164	0.86[EUR][1000 genomes]
rs35864597	0.82[ASN][1000 genomes]
rs4853016	0.86[EUR][1000 genomes]
rs6546894	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs702462	0.86[EUR][1000 genomes]
rs702466	0.81[ASN][1000 genomes]
rs7340453	0.85[EUR][1000 genomes]
rs7559252	0.88[ASN][1000 genomes]
rs8001	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs828853	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs828855	0.84[EUR][1000 genomes]
rs828856	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs828857	0.86[EUR][1000 genomes]
rs828858	0.86[EUR][1000 genomes]
rs828859	0.85[EUR][1000 genomes]
rs828882	0.82[ASN][1000 genomes]
rs828883	0.82[ASN][1000 genomes]
rs828884	0.80[ASN][1000 genomes]
rs828886	0.80[ASN][1000 genomes]
rs828888	0.80[ASN][1000 genomes]
rs828889	0.82[ASN][1000 genomes]
rs828903	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs844168	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
3	nsv834261	chr2:74391709-74613720	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74427200-74432600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:74427200-74433600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:74427200-74433600	Weak transcription	Lung	lung
4	chr2:74427200-74438200	Weak transcription	Fetal Kidney	kidney
5	chr2:74427400-74432800	Weak transcription	Gastric	stomach
6	chr2:74427400-74432800	Weak transcription	Right Atrium	heart
7	chr2:74427400-74432800	Weak transcription	Thymus	Thymus
8	chr2:74427400-74433400	Weak transcription	Esophagus	oesophagus
9	chr2:74427400-74435400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:74427400-74441000	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:74427400-74441200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:74427400-74448400	Weak transcription	Brain Anterior Caudate	brain
13	chr2:74427400-74453000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:74427400-74453200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:74427400-74460200	Weak transcription	Brain Substantia Nigra	brain
16	chr2:74427400-74462000	Weak transcription	Brain Angular Gyrus	brain
17	chr2:74427400-74484400	Weak transcription	Fetal Lung	lung
18	chr2:74427600-74432600	Weak transcription	Primary B cells from cord blood	blood
19	chr2:74427600-74435200	Weak transcription	Fetal Brain Female	brain
20	chr2:74427600-74435600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:74427600-74436600	Weak transcription	Right Ventricle	heart
22	chr2:74427600-74442600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:74427800-74433400	Weak transcription	NH-A	brain
24	chr2:74427800-74435000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:74427800-74494200	Weak transcription	Brain Germinal Matrix	brain
26	chr2:74428000-74435200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr2:74428000-74435200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:74428000-74448600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:74428600-74449600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:74428800-74432800	Weak transcription	Left Ventricle	heart
31	chr2:74428800-74433000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:74429000-74435000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:74429000-74450600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:74429000-74453200	Weak transcription	Ovary	ovary
35	chr2:74429200-74433000	Weak transcription	Stomach Mucosa	stomach
36	chr2:74429200-74433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:74429200-74433800	Genic enhancers	Dnd41	blood
38	chr2:74429200-74452800	Weak transcription	Fetal Heart	heart
39	chr2:74429400-74433000	Weak transcription	NHLF	lung
40	chr2:74429400-74433200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:74429600-74432800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:74429600-74432800	Weak transcription	NHDF-Ad	bronchial
43	chr2:74429600-74433200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:74429600-74433600	Weak transcription	HSMMtube	muscle
45	chr2:74430200-74432600	Strong transcription	Osteobl	bone
46	chr2:74430200-74433200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:74430200-74433800	Genic enhancers	H1 Cell Line	embryonic stem cell
48	chr2:74430200-74433800	Genic enhancers	K562	blood
49	chr2:74430600-74433600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr2:74431200-74433800	Genic enhancers	HepG2	liver

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