Variant report

Variant	rs16848110
Chromosome Location	chr1:227934606-227934607
allele	G/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:4)
LncRNA
region (count:3)
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	POLR2A	chr1:227934449-227938226	PBDE	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
2	chr1:227932601..227934786-chr1:227948065..227950535,2	MCF-7	breast:
3	chr1:227916288..227917792-chr1:227932623..227935322,2	K562	blood:
4	chr1:227921956..227924183-chr1:227932541..227935696,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JMJD4-1	chr1:227933476-227934895	ENSG00000251190
2	lnc-PRSS38-1	chr1:227933476-227934892	ENSG00000230005.1
3	lnc-JMJD4-1	chr1:227933476-227934892	ENSG00000230005.2

No data

Variant related genes	Relation type
SNAP47	TF binding region
ENSG00000081692	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12566948	0.89[CEU][hapmap]
rs1570429	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs17851681	0.88[CEU][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2029836	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2031132	0.81[CEU][hapmap]
rs2273936	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3806264	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs41270161	0.96[EUR][1000 genomes]
rs41270167	0.97[EUR][1000 genomes]
rs41305134	0.84[EUR][1000 genomes]
rs4837	0.96[EUR][1000 genomes]
rs58565844	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748405	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer 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
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16848110	C1orf142	Cis_1M	lymphoblastoid	RTeQTL
rs16848110	C1orf35	cis	parietal	SCAN
rs16848110	HIST3H2A	cis	parietal	SCAN
rs16848110	ZNF678	cis	Muscle Skeletal	GTEx
rs16848110	HIST3H2A	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227923800-227935600	Weak transcription	Aorta	Aorta
2	chr1:227924000-227935400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227924000-227935600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr1:227924000-227936400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:227924200-227934800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:227924200-227935000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:227924200-227935000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:227924200-227935000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:227924200-227935400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:227924200-227935400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:227924200-227935400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:227924200-227935400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:227924200-227935400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:227924200-227935400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:227924200-227935400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr1:227924200-227935400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:227924200-227935600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:227924200-227935600	Weak transcription	Primary B cells from cord blood	blood
19	chr1:227924200-227935800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:227924200-227935800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:227924200-227935800	Weak transcription	A549	lung
22	chr1:227924200-227936000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:227924200-227936000	Weak transcription	Fetal Kidney	kidney
24	chr1:227924200-227940800	Weak transcription	HSMMtube	muscle
25	chr1:227924200-227941200	Weak transcription	HSMM	muscle
26	chr1:227924200-227941200	Weak transcription	NHDF-Ad	bronchial
27	chr1:227924200-227941600	Weak transcription	Osteobl	bone
28	chr1:227924200-227942000	Weak transcription	Hela-S3	cervix
29	chr1:227924200-227946800	Weak transcription	HUVEC	blood vessel
30	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:227924400-227935400	Weak transcription	Fetal Lung	lung
32	chr1:227924400-227935800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:227924400-227936200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:227924600-227935400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:227924800-227935000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:227924800-227935400	Weak transcription	Brain Substantia Nigra	brain
37	chr1:227924800-227935600	Weak transcription	Colonic Mucosa	Colon
38	chr1:227924800-227941400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:227925000-227935000	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:227925000-227935200	Weak transcription	Liver	Liver
41	chr1:227925000-227935400	Weak transcription	Adipose Nuclei	Adipose
42	chr1:227925000-227935400	Weak transcription	K562	blood
43	chr1:227925000-227935600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:227925000-227936000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:227925000-227941400	Weak transcription	Fetal Brain Male	brain
46	chr1:227925200-227934800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:227925200-227935400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:227925200-227935600	Weak transcription	HepG2	liver
49	chr1:227925200-227941200	Weak transcription	Psoas Muscle	Psoas
50	chr1:227925400-227935600	Weak transcription	Brain Hippocampus Middle	brain

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