Variant report

Variant	rs12442168
Chromosome Location	chr15:44204047-44204048
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr15:44203180-44204287	IMR90	lung:	n/a	n/a
2	PBX3	chr15:44203183-44204047	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr15:44203082-44204093	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr15:44203141-44204103	SK-N-SH	brain:	n/a	n/a
5	RXRA	chr15:44203206-44204076	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr15:44203246-44204059	HUVEC	blood vessel:	n/a	n/a
7	NFIC	chr15:44203295-44204125	ECC-1	luminal epithelium:	n/a	n/a
8	GATA3	chr15:44203085-44204080	SK-N-SH	brain:	n/a	n/a
9	EP300	chr15:44203116-44204090	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr15:44203165-44204082	SK-N-SH	brain:	n/a	n/a
11	EP300	chr15:44203241-44204086	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44203028..44205374-chr15:44210387..44212773,2	K562	blood:
2	chr15:44202676..44204581-chr15:44827219..44829622,2	K562	blood:

No data

Variant related genes	Relation type
FRMD5	TF binding region
ENSG00000179523	Chromatin interaction
ENSG00000171877	Chromatin interaction
ENSG00000104131	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1008183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1077421	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11070413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070416	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11630936	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11631901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11635039	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11637468	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12439442	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12440402	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16944774	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945686	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs16950215	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306674	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28377221	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28438984	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28525216	1.00[TSI][hapmap]
rs28542819	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28599486	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28685813	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28706414	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3742981	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3850777	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55927923	0.97[EUR][1000 genomes]
rs60484809	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7167976	0.82[CHB][hapmap]
rs7178452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9806129	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9920164	1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a
6	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12442168	LOC440278	cis	multi-tissue	Pritchard
rs12442168	ELL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44156800-44206400	Weak transcription	Fetal Brain Male	brain
2	chr15:44173600-44208000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:44173800-44211600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:44174200-44211600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:44191200-44207400	Weak transcription	Ovary	ovary
6	chr15:44194600-44208200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:44196400-44204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:44196400-44205200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:44196400-44207600	Weak transcription	Gastric	stomach
10	chr15:44196400-44208000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:44196400-44212200	Weak transcription	Fetal Stomach	stomach
12	chr15:44196400-44216800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:44196600-44204600	Weak transcription	Hela-S3	cervix
14	chr15:44196600-44205400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:44196600-44208200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:44198000-44205200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:44198000-44211600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:44198200-44217600	Weak transcription	Brain Germinal Matrix	brain
19	chr15:44198400-44208000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:44198600-44205400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:44198800-44207600	Weak transcription	Fetal Brain Female	brain
22	chr15:44200000-44208000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:44201200-44208000	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:44201400-44205400	Weak transcription	Adipose Nuclei	Adipose
25	chr15:44201400-44209000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:44201800-44208400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:44202000-44206800	Enhancers	NHDF-Ad	bronchial
28	chr15:44202400-44204600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:44202400-44206200	Enhancers	Brain Angular Gyrus	brain
30	chr15:44202400-44206400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:44202400-44206400	Enhancers	NHLF	lung
32	chr15:44202400-44206800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:44202800-44205200	Enhancers	HUVEC	blood vessel
34	chr15:44203000-44204400	Enhancers	Osteobl	bone
35	chr15:44203000-44206200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:44203000-44206200	Enhancers	Brain Anterior Caudate	brain
37	chr15:44203000-44206400	Enhancers	Brain Substantia Nigra	brain
38	chr15:44203000-44206600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr15:44203000-44206800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:44203000-44206800	Enhancers	NH-A	brain
41	chr15:44203200-44204400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:44203200-44204800	Genic enhancers	HMEC	breast
43	chr15:44203200-44205400	Enhancers	Right Atrium	heart
44	chr15:44203200-44206000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr15:44203200-44206400	Enhancers	HSMM	muscle
46	chr15:44203200-44206800	Enhancers	NHEK	skin
47	chr15:44203200-44208600	Enhancers	Brain Hippocampus Middle	brain
48	chr15:44203400-44206200	Enhancers	Brain Cingulate Gyrus	brain
49	chr15:44203400-44206200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:44203400-44206200	Enhancers	HSMMtube	muscle

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