Variant report

Variant	rs1151756
Chromosome Location	chr1:62151773-62151774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62151673..62154545-chr1:62190417..62192026,2	K562	blood:

Variant related genes	Relation type
ENSG00000162604	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11207807	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207808	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151757	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151759	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151770	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]
rs1151771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151775	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1151776	0.92[EUR][1000 genomes]
rs12117475	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130241	0.87[EUR][1000 genomes]
rs12130439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12134102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134428	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12137410	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12141280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12141298	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143420	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12144284	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1286624	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1286625	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1286626	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1286628	0.94[EUR][1000 genomes]
rs1286629	0.94[EUR][1000 genomes]
rs1286630	0.94[EUR][1000 genomes]
rs1286634	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1611797	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1620169	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1692131	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17378384	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779267	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2051135	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2051136	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2799626	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4443919	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6666057	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6691402	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697770	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6698656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72672375	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72672390	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72674608	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7536565	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7538825	0.95[EUR][1000 genomes]
rs7539026	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7550631	0.89[EUR][1000 genomes];0.86[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	nsv947264	chr1:62146171-62151947	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1151756	TM2D1	cis	parietal	SCAN
rs1151756	TM2D1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62126000-62165200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:62131600-62163800	Weak transcription	Thymus	Thymus
3	chr1:62134800-62164400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:62134800-62164400	Weak transcription	Right Ventricle	heart
5	chr1:62135000-62165000	Weak transcription	Brain Germinal Matrix	brain
6	chr1:62136000-62153400	Weak transcription	NHDF-Ad	bronchial
7	chr1:62136600-62151800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:62136800-62173800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:62138800-62189600	Weak transcription	Psoas Muscle	Psoas
10	chr1:62140000-62189000	Weak transcription	NHLF	lung
11	chr1:62140200-62163800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:62142800-62157800	Weak transcription	A549	lung
13	chr1:62142800-62172200	Weak transcription	Ovary	ovary
14	chr1:62142800-62188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:62143200-62157800	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:62143200-62164000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:62143400-62153000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:62143600-62163400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:62143800-62152600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:62143800-62165600	Weak transcription	Stomach Mucosa	stomach
21	chr1:62143800-62170200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:62144000-62153000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:62144200-62162800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:62144600-62163800	Weak transcription	Spleen	Spleen
25	chr1:62144600-62164800	Weak transcription	Fetal Brain Female	brain
26	chr1:62144600-62165000	Weak transcription	Brain Substantia Nigra	brain
27	chr1:62144600-62165600	Weak transcription	HepG2	liver
28	chr1:62144800-62153000	Strong transcription	Liver	Liver
29	chr1:62144800-62161400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:62144800-62161600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:62144800-62163000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:62144800-62164400	Weak transcription	Fetal Brain Male	brain
33	chr1:62145000-62162600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:62145000-62163000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:62145000-62164800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:62145000-62165000	Weak transcription	NH-A	brain
37	chr1:62145000-62172200	Weak transcription	Colonic Mucosa	Colon
38	chr1:62145200-62167400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:62145800-62153000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:62145800-62153200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:62146000-62153200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:62146000-62153600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:62146000-62163600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:62146200-62152800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:62146200-62153000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr1:62146200-62154200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:62146200-62163800	Weak transcription	HSMMtube	muscle
48	chr1:62146200-62190200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:62146400-62164200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:62146400-62166000	Weak transcription	Brain Angular Gyrus	brain

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