Variant report

Variant	rs4657481
Chromosome Location	chr1:165822891-165822892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165822136..165824706-chr1:165825180..165827276,2	K562	blood:
2	chr1:165738096..165740327-chr1:165822815..165825258,2	MCF-7	breast:
3	chr1:165804707..165808619-chr1:165822123..165824856,3	K562	blood:
4	chr1:165822075..165824045-chr1:165844384..165846604,2	K562	blood:
5	chr1:165804707..165809840-chr1:165822123..165825220,4	K562	blood:

Variant related genes	Relation type
ENSG00000143183	Chromatin interaction
ENSG00000224358	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10737519	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753694	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10800162	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10918291	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10918294	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590711	0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12041574	0.87[CHB][hapmap]
rs1934275	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2185268	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34800847	0.94[ASN][1000 genomes]
rs4483381	0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4535982	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4548416	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6426941	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6677965	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[YRI][hapmap];0.91[ASN][1000 genomes]
rs6678380	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.91[ASN][1000 genomes]
rs6682894	0.93[ASN][1000 genomes]
rs6684773	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6686237	0.87[ASN][1000 genomes]
rs6690966	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6702462	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7517175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539793	0.85[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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv2830094	chr1:165785503-165840411	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
3	nsv548097	chr1:165797966-165825166	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
4	esv2755529	chr1:165813862-165858354	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv437246	chr1:165822891-165860813	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4657481	TOMM40L	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165812200-165823200	Weak transcription	Aorta	Aorta
2	chr1:165812200-165823200	Weak transcription	Fetal Stomach	stomach
3	chr1:165812200-165823400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:165812400-165823200	Weak transcription	Left Ventricle	heart
5	chr1:165812400-165823200	Weak transcription	Right Ventricle	heart
6	chr1:165812400-165823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:165813000-165823200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:165814000-165823200	Weak transcription	Small Intestine	intestine
9	chr1:165816200-165825000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:165817600-165823800	Enhancers	Fetal Thymus	thymus
11	chr1:165818000-165829200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:165818400-165823800	Enhancers	Thymus	Thymus
13	chr1:165818600-165823200	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:165818600-165828000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:165818800-165823400	Weak transcription	Right Atrium	heart
16	chr1:165818800-165824800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:165818800-165826600	Weak transcription	Esophagus	oesophagus
18	chr1:165819000-165823200	Weak transcription	Adipose Nuclei	Adipose
19	chr1:165819000-165826000	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:165819000-165826200	Weak transcription	Stomach Mucosa	stomach
21	chr1:165819200-165823000	Weak transcription	Hela-S3	cervix
22	chr1:165819200-165824600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:165819200-165824800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:165819600-165824400	Enhancers	HMEC	breast
25	chr1:165820200-165825800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:165820400-165825200	Enhancers	Fetal Heart	heart
27	chr1:165820400-165827600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr1:165820600-165823200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:165820600-165823200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:165820600-165823200	Weak transcription	Fetal Intestine Small	intestine
31	chr1:165820800-165823000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:165820800-165823200	Weak transcription	Placenta	Placenta
33	chr1:165820800-165823200	Weak transcription	Gastric	stomach
34	chr1:165820800-165823200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:165820800-165824800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:165820800-165828000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:165821000-165823200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr1:165821000-165823200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:165821000-165823200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:165821000-165823200	Weak transcription	Fetal Intestine Large	intestine
41	chr1:165821000-165823400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:165821000-165825800	Enhancers	H1 Cell Line	embryonic stem cell
43	chr1:165821000-165832200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:165821200-165823200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:165821200-165823200	Weak transcription	Pancreas	Pancrea
46	chr1:165821200-165823400	Weak transcription	Spleen	Spleen
47	chr1:165821400-165827200	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr1:165821600-165823200	Enhancers	A549	lung
49	chr1:165821600-165823800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:165821600-165823800	Enhancers	K562	blood

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