Variant report

Variant	rs1151775
Chromosome Location	chr1:62191593-62191594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:62190149-62191715	GM12891	blood:	n/a	n/a
2	TBL1XR1	chr1:62190386-62191808	K562	blood:	n/a	n/a
3	HCFC1	chr1:62190072-62191604	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:62189227-62191608	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:62190879-62191670	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:62189843-62191858	Hela-S3	cervix:	n/a	n/a
7	CUX1	chr1:62190228-62191614	K562	blood:	n/a	n/a
8	MXI1	chr1:62190456-62191708	GM12878	blood:	n/a	n/a
9	MYC	chr1:62190288-62191643	K562	blood:	n/a	n/a
10	NFYA	chr1:62190759-62191617	Hela-S3	cervix:	n/a	chr1:62191069-62191082
11	JUN	chr1:62190190-62191809	K562	blood:	n/a	chr1:62190429-62190438

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:62190630..62191606-chr1:62207469..62208515,4	Hela-S3	cervix:
2	chr1:62148615..62150124-chr1:62189264..62192017,2	MCF-7	breast:
3	chr1:62190320..62192154-chr1:62900473..62901978,2	MCF-7	breast:
4	chr1:62173473..62177807-chr1:62188633..62191997,6	K562	blood:
5	chr1:62149064..62151297-chr1:62189288..62192078,2	K562	blood:
6	chr1:62188914..62195188-chr1:62202056..62212232,19	MCF-7	breast:
7	chr1:62187463..62192137-chr1:62206143..62210486,9	MCF-7	breast:

No data

Variant related genes	Relation type
TM2D1	TF binding region
ENSG00000132849	Chromatin interaction
ENSG00000162607	Chromatin interaction
ENSG00000271200	Chromatin interaction
ENSG00000162604	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11207807	0.88[EUR][1000 genomes]
rs11207808	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11207811	0.87[YRI][hapmap]
rs1151756	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]
rs1151757	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1151759	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1151762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1151770	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]
rs1151771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1151776	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12117475	0.88[EUR][1000 genomes]
rs12124430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12130241	0.90[EUR][1000 genomes];1.00[ASN][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];0.93[ASN][1000 genomes]
rs12134102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12134205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12134428	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12137410	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12141280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141298	0.89[EUR][1000 genomes]
rs12143420	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12144284	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1286624	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1286625	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1286626	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1286628	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286629	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286630	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286634	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1611797	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1620169	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1692131	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17378384	0.88[EUR][1000 genomes]
rs1779267	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2051135	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2051136	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2799626	0.94[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];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4443919	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61770089	0.84[AFR][1000 genomes]
rs6662941	0.85[ASN][1000 genomes]
rs6666057	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6691402	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6697770	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6698656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs72672375	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72672390	0.88[EUR][1000 genomes]
rs72674608	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7517261	0.81[AFR][1000 genomes]
rs7536565	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7538825	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7539026	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7550631	0.89[EUR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1151775	TM2D1	cis	parietal	SCAN
rs1151775	TM2D1	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62189200-62191600	Active TSS	K562	blood
2	chr1:62189400-62191600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:62189400-62191600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:62189400-62191600	Active TSS	Fetal Lung	lung
5	chr1:62189400-62191800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:62189400-62191800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:62189400-62191800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:62189600-62191600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:62189600-62191600	Active TSS	Brain Angular Gyrus	brain
10	chr1:62189600-62191600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr1:62189600-62191600	Active TSS	Right Atrium	heart
12	chr1:62189600-62191600	Active TSS	Stomach Smooth Muscle	stomach
13	chr1:62189600-62191600	Active TSS	A549	lung
14	chr1:62189600-62191600	Active TSS	NHDF-Ad	bronchial
15	chr1:62189800-62191600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr1:62189800-62191600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:62189800-62191600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:62189800-62191600	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:62189800-62191600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:62189800-62191600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:62189800-62191600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr1:62189800-62191800	Active TSS	GM12878-XiMat	blood
23	chr1:62190000-62191600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:62190000-62191600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:62190000-62191600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:62190000-62191600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:62190000-62191600	Active TSS	Aorta	Aorta
28	chr1:62190000-62191600	Active TSS	Brain Anterior Caudate	brain
29	chr1:62190000-62191600	Active TSS	Fetal Intestine Small	intestine
30	chr1:62190000-62191600	Active TSS	Fetal Stomach	stomach
31	chr1:62190000-62191600	Active TSS	Rectal Smooth Muscle	rectum
32	chr1:62190000-62191600	Active TSS	NHEK	skin
33	chr1:62190200-62191600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:62190200-62191600	Active TSS	Brain Hippocampus Middle	brain
35	chr1:62190200-62191600	Active TSS	Brain Substantia Nigra	brain
36	chr1:62190200-62191600	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr1:62190200-62191600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr1:62190200-62191600	Active TSS	Fetal Muscle Leg	muscle
39	chr1:62190200-62191600	Active TSS	Fetal Thymus	thymus
40	chr1:62190200-62191600	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr1:62190200-62191600	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr1:62190200-62191800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr1:62190200-62191800	Active TSS	Colon Smooth Muscle	Colon
44	chr1:62190400-62191600	Active TSS	Liver	Liver
45	chr1:62190400-62191600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:62190600-62191600	Active TSS	Primary T cells fromperipheralblood	blood
47	chr1:62190800-62191600	Active TSS	Brain Germinal Matrix	brain
48	chr1:62190800-62191600	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr1:62191000-62191600	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr1:62191000-62191600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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