Variant report

Variant	rs1151770
Chromosome Location	chr1:62175340-62175341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:62175249-62175768	A549	lung:	n/a	chr1:62175399-62175410 chr1:62175401-62175410 chr1:62175401-62175412 chr1:62175632-62175645 chr1:62175471-62175484
2	CEBPB	chr1:62174921-62175603	K562	blood:	n/a	chr1:62175399-62175410 chr1:62175401-62175410 chr1:62175401-62175412 chr1:62175471-62175484
3	GATA1	chr1:62174585-62175558	K562	blood:	n/a	n/a
4	CEBPB	chr1:62175283-62175479	MCF-7	breast:	n/a	chr1:62175399-62175410 chr1:62175401-62175410 chr1:62175401-62175412
5	CEBPB	chr1:62175236-62175577	HepG2	liver:	n/a	chr1:62175399-62175410 chr1:62175401-62175410 chr1:62175401-62175412 chr1:62175471-62175484
6	CEBPB	chr1:62175218-62175577	IMR90	lung:	n/a	chr1:62175399-62175410 chr1:62175401-62175410 chr1:62175401-62175412 chr1:62175471-62175484
7	CUX1	chr1:62174620-62175475	K562	blood:	n/a	n/a
8	JUND	chr1:62174591-62175400	K562	blood:	n/a	n/a
9	MAFK	chr1:62174640-62175409	K562	blood:	n/a	n/a
10	CEBPB	chr1:62175241-62175566	Hela-S3	cervix:	n/a	chr1:62175399-62175410 chr1:62175401-62175410 chr1:62175401-62175412 chr1:62175471-62175484
11	CEBPB	chr1:62175151-62175586	K562	blood:	n/a	chr1:62175399-62175410 chr1:62175401-62175410 chr1:62175401-62175412 chr1:62175471-62175484
12	EP300	chr1:62174631-62175472	K562	blood:	n/a	chr1:62175219-62175226 chr1:62175400-62175414
13	ARID3A	chr1:62174652-62175699	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:62173080..62176930-chr1:62205875..62209587,4	MCF-7	breast:
2	chr1:62173473..62177807-chr1:62188633..62191997,6	K562	blood:
3	chr1:62172803..62176394-chr1:62188013..62191041,5	K562	blood:

Variant related genes	Relation type
TM2D1	TF binding region
ENSG00000132849	Chromatin interaction
ENSG00000162604	Chromatin interaction
ENSG00000271200	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11207807	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11207808	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151756	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151757	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151759	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151762	0.94[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151771	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151773	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151775	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1151776	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12117475	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12124430	0.94[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130241	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12130439	0.94[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134102	0.94[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12134205	0.94[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12134428	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137410	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141280	0.94[CEU][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12141298	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12143420	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs12144284	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286624	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286625	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286626	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286628	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1286629	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1286630	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1286634	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1611797	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1620169	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1692131	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1692132	0.81[EUR][1000 genomes]
rs17378384	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1779267	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051135	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051136	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799626	0.88[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443919	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662941	0.93[ASN][1000 genomes]
rs6666057	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691402	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6697770	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6698656	0.93[ASN][1000 genomes]
rs72672375	0.81[EUR][1000 genomes]
rs72672390	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72674608	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536565	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538825	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7539026	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550631	0.91[EUR][1000 genomes];1.00[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	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3444616	chr1:62175256-62175511	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1151770	TM2D1	cis	parietal	SCAN
rs1151770	TM2D1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62138800-62189600	Weak transcription	Psoas Muscle	Psoas
2	chr1:62140000-62189000	Weak transcription	NHLF	lung
3	chr1:62142800-62188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:62146200-62190200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:62158600-62189800	Weak transcription	Pancreas	Pancrea
6	chr1:62161200-62180600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:62161800-62179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:62162600-62177400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:62163400-62181800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:62165000-62175800	Weak transcription	Right Atrium	heart
11	chr1:62165000-62189800	Weak transcription	Aorta	Aorta
12	chr1:62165400-62189400	Weak transcription	Fetal Brain Male	brain
13	chr1:62165400-62189600	Weak transcription	Right Ventricle	heart
14	chr1:62165400-62189800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:62166400-62176600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:62166400-62176600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:62166400-62189400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:62166600-62187400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:62166600-62189400	Weak transcription	A549	lung
20	chr1:62166800-62178000	Weak transcription	Brain Angular Gyrus	brain
21	chr1:62166800-62189400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:62167600-62177200	Weak transcription	Brain Substantia Nigra	brain
23	chr1:62168400-62177600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:62169000-62176000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr1:62169600-62175400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:62169600-62175400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:62169600-62177400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:62169600-62179400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:62169600-62179600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:62169600-62181200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:62169800-62175400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:62169800-62175400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:62169800-62175400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:62169800-62175800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:62169800-62176000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:62170000-62175600	Strong transcription	Fetal Thymus	thymus
37	chr1:62170000-62175800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:62170000-62175800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:62170000-62179200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:62170200-62175800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:62170400-62175400	Strong transcription	Fetal Lung	lung
42	chr1:62170400-62175800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:62170400-62176000	Strong transcription	Primary T cells from cord blood	blood
44	chr1:62170600-62175800	Strong transcription	NHDF-Ad	bronchial
45	chr1:62170600-62176000	Strong transcription	Dnd41	blood
46	chr1:62170600-62176200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:62171000-62175600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:62171200-62175400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:62171600-62188400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:62172000-62189400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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