Variant report

Variant	rs12025248
Chromosome Location	chr1:95154279-95154280
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95116283..95118037-chr1:95153158..95155389,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC44A3-2	chr1:95153449-95155440	XLOC_000303

Variant related genes	Relation type
ENSG00000232857	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10782989	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10874875	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10874876	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10874877	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165213	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12021681	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12025489	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12040641	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12046216	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048933	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1689173	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1689178	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6669784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6677368	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685841	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs841326	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs841357	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	esv2756851	chr1:95119790-95158603	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2758950	chr1:95119790-95158603	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv998738	chr1:95126536-95155399	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv546853	chr1:95127463-95154279	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv871001	chr1:95128546-95171891	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv436535	chr1:95128791-95155240	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1013700	chr1:95130666-95155387	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1013561	chr1:95130666-95155399	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1012925	chr1:95130666-95155534	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv999580	chr1:95130666-95155585	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv2421913	chr1:95130678-95154279	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv2764194	chr1:95130678-95155597	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1002560	chr1:95130754-95155387	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1013295	chr1:95130754-95155399	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv442927	chr1:95130766-95155399	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv1011128	chr1:95130788-95155399	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv1000486	chr1:95131596-95155399	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	esv3692780	chr1:95131929-95154279	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv546856	chr1:95131929-95154279	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv513993	chr1:95132532-95154956	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	esv12694	chr1:95134798-95156000	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv462550	chr1:95136071-95154279	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
24	nsv462561	chr1:95136071-95154279	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
25	nsv546858	chr1:95136071-95154279	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
26	nsv871916	chr1:95143999-95189230	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
27	nsv437228	chr1:95146564-95164436	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12025248	MTF2	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95126800-95164200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:95128400-95154600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:95135000-95154400	Weak transcription	NHLF	lung
4	chr1:95140000-95155600	Weak transcription	HSMMtube	muscle
5	chr1:95142800-95167800	Weak transcription	Pancreas	Pancrea
6	chr1:95143800-95154400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:95145200-95157200	Weak transcription	Fetal Intestine Large	intestine
8	chr1:95145200-95163600	Weak transcription	Stomach Mucosa	stomach
9	chr1:95150800-95154400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:95151200-95160600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:95151400-95165800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:95152800-95154400	Weak transcription	NHDF-Ad	bronchial
13	chr1:95152800-95156000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:95152800-95195000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:95153000-95154400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:95153000-95154600	Weak transcription	Adipose Nuclei	Adipose
17	chr1:95153000-95155400	Weak transcription	NHEK	skin
18	chr1:95153000-95157000	Weak transcription	Fetal Intestine Small	intestine
19	chr1:95153000-95157600	Weak transcription	Right Atrium	heart
20	chr1:95153000-95173000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:95153400-95156000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:95153400-95167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:95153600-95155000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:95153800-95156000	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr1:95154000-95154400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr1:95154000-95154400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr1:95154000-95154600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:95154000-95155000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:95154000-95155000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr1:95154000-95155000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr1:95154000-95155600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr1:95154000-95156000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:95154000-95156200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr1:95154000-95157600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr1:95154200-95154800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:95154200-95154800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:95154200-95155000	Enhancers	HepG2	liver
38	chr1:95154200-95155400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:95154200-95156000	Enhancers	HSMM	muscle
40	chr1:95154200-95157200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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