Variant report

Variant	rs12143420
Chromosome Location	chr1:62163715-62163716
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62162809..62165053-chr1:62166918..62169427,2	K562	blood:
2	chr1:62157037..62159545-chr1:62162832..62164791,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11207807	0.93[ASN][1000 genomes]
rs11207808	0.93[ASN][1000 genomes]
rs1151756	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1151757	0.93[ASN][1000 genomes]
rs1151759	0.93[ASN][1000 genomes]
rs1151762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1151770	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs1151771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1151773	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1151775	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12117475	0.93[ASN][1000 genomes]
rs12124430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12130439	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs12134102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12134205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12141280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12141298	0.93[ASN][1000 genomes]
rs17378384	0.93[ASN][1000 genomes]
rs1779267	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2799626	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6662941	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6691402	0.93[ASN][1000 genomes]
rs6698656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72672375	0.85[ASN][1000 genomes]
rs72672390	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12143420	TM2D1	cis	cerebellum	SCAN

Chromatin state (count:124 , 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	chr1:62136800-62173800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:62138800-62189600	Weak transcription	Psoas Muscle	Psoas
8	chr1:62140000-62189000	Weak transcription	NHLF	lung
9	chr1:62140200-62163800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:62142800-62172200	Weak transcription	Ovary	ovary
11	chr1:62142800-62188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:62143200-62164000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:62143800-62165600	Weak transcription	Stomach Mucosa	stomach
14	chr1:62143800-62170200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:62144600-62163800	Weak transcription	Spleen	Spleen
16	chr1:62144600-62164800	Weak transcription	Fetal Brain Female	brain
17	chr1:62144600-62165000	Weak transcription	Brain Substantia Nigra	brain
18	chr1:62144600-62165600	Weak transcription	HepG2	liver
19	chr1:62144800-62164400	Weak transcription	Fetal Brain Male	brain
20	chr1:62145000-62164800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:62145000-62165000	Weak transcription	NH-A	brain
22	chr1:62145000-62172200	Weak transcription	Colonic Mucosa	Colon
23	chr1:62145200-62167400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:62146200-62163800	Weak transcription	HSMMtube	muscle
25	chr1:62146200-62190200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:62146400-62164200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:62146400-62166000	Weak transcription	Brain Angular Gyrus	brain
28	chr1:62146600-62164000	Weak transcription	Gastric	stomach
29	chr1:62146600-62164800	Weak transcription	Esophagus	oesophagus
30	chr1:62146600-62165200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:62146600-62166000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:62147000-62164400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:62147200-62164800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:62147600-62173400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:62148000-62164800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:62148400-62165200	Weak transcription	Fetal Kidney	kidney
37	chr1:62149600-62164000	Weak transcription	Aorta	Aorta
38	chr1:62149600-62165000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:62150000-62163800	Weak transcription	Brain Anterior Caudate	brain
40	chr1:62150200-62164800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:62150200-62164800	Weak transcription	K562	blood
42	chr1:62150200-62165200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:62150200-62165200	Weak transcription	Fetal Lung	lung
44	chr1:62150200-62165600	Weak transcription	Small Intestine	intestine
45	chr1:62151400-62164400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:62152200-62164200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:62152400-62175200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:62152800-62164000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:62152800-62164400	Weak transcription	Lung	lung
50	chr1:62154200-62164400	Weak transcription	Muscle Satellite Cultured Cells	--

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