Variant report

Variant	rs10089487
Chromosome Location	chr8:38858484-38858485
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	FOSL2	chr8:38858275-38859269	A549	lung:	n/a	chr8:38858422-38858431
2	CHD1	chr8:38852795-38859264	IMR90	lung:	n/a	chr8:38854280-38854290 chr8:38854954-38854964
3	GATA2	chr8:38856987-38859131	HUVEC	blood vessel:	n/a	n/a
4	GATA3	chr8:38858274-38859446	A549	lung:	n/a	n/a
5	FOS	chr8:38858474-38859117	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr8:38857757-38859185	HUVEC	blood vessel:	n/a	n/a
7	STAT3	chr8:38858352-38858497	MCF10A-Er-Src	breast:	n/a	n/a
8	EP300	chr8:38858438-38859148	SK-N-SH	brain:	n/a	chr8:38858859-38858869
9	POLR2A	chr8:38858214-38859158	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr8:38857932-38859139	HUVEC	blood vessel:	n/a	n/a
11	BCL3	chr8:38858439-38859247	A549	lung:	n/a	n/a
12	EP300	chr8:38858454-38859315	A549	lung:	n/a	chr8:38858859-38858869
13	GATA3	chr8:38858319-38859289	SK-N-SH	brain:	n/a	n/a
14	SP1	chr8:38856339-38859288	A549	lung:	n/a	n/a
15	TCF12	chr8:38858396-38859254	SK-N-SH	brain:	n/a	n/a
16	EP300	chr8:38858278-38859315	A549	lung:	n/a	chr8:38858419-38858433 chr8:38858859-38858869
17	GATA3	chr8:38858365-38859186	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr8:38854896-38859164	HUVEC	blood vessel:	n/a	n/a
19	MAX	chr8:38858434-38859278	A549	lung:	n/a	n/a
20	POLR2A	chr8:38855026-38859169	HUVEC	blood vessel:	n/a	n/a
21	TCF12	chr8:38853459-38859347	A549	lung:	n/a	chr8:38853682-38853690 chr8:38854813-38854820
22	PBX3	chr8:38858378-38859242	SK-N-SH	brain:	n/a	n/a
23	SIX5	chr8:38858245-38859131	A549	lung:	n/a	n/a
24	REST	chr8:38858263-38859230	A549	lung:	n/a	n/a
25	SP1	chr8:38858381-38859251	A549	lung:	n/a	n/a
26	GATA3	chr8:38858465-38859215	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:38856826..38859687-chr8:38879245..38881053,2	MCF-7	breast:
2	chr8:38849585..38851368-chr8:38856687..38858833,2	MCF-7	breast:
3	chr8:38853560..38856920-chr8:38856982..38859048,5	K562	blood:
4	chr8:38839827..38841978-chr8:38857481..38860325,2	K562	blood:

Variant related genes	Relation type
TM2D2	TF binding region
ENSG00000168615	Chromatin interaction
ENSG00000169490	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10086693	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10105311	0.93[ASN][1000 genomes]
rs10106085	1.00[CEU][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113077	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10958813	0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs11777376	0.83[EUR][1000 genomes]
rs11784624	0.80[CHD][hapmap];0.83[MEX][hapmap]
rs11787126	0.94[JPT][hapmap]
rs12056655	0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs12541231	0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs12548006	0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs12548948	0.94[JPT][hapmap]
rs12549547	0.94[JPT][hapmap]
rs13256952	0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs13268394	0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs13274567	0.94[JPT][hapmap]
rs13282047	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28641150	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4128871	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129095	0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs4236755	0.90[MEX][hapmap];0.83[TSI][hapmap]
rs4236757	0.81[MEX][hapmap]
rs4269506	0.83[MEX][hapmap]
rs4308699	0.86[MEX][hapmap];0.83[TSI][hapmap]
rs4495395	0.83[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4517088	0.83[MEX][hapmap]
rs4543512	0.94[JPT][hapmap]
rs4601278	0.91[MEX][hapmap];0.81[TSI][hapmap]
rs4615534	0.82[MEX][hapmap]
rs4733894	0.88[ASN][1000 genomes]
rs4733897	0.80[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs4733905	0.86[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs4733959	0.82[JPT][hapmap]
rs4733964	0.80[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6474515	0.89[ASN][1000 genomes]
rs6474516	0.89[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs6981759	0.86[ASN][1000 genomes]
rs6991383	0.84[CHD][hapmap];0.83[MEX][hapmap]
rs7000059	0.88[ASN][1000 genomes]
rs7010131	0.89[ASN][1000 genomes]
rs7015505	0.84[CHD][hapmap]
rs7821237	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7832578	0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7838874	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7840044	0.81[CHD][hapmap];0.83[MEX][hapmap]
rs9643904	0.86[GIH][hapmap];0.94[JPT][hapmap]
rs9643906	0.93[JPT][hapmap]
rs9650347	0.83[MEX][hapmap]
rs9987126	0.80[CHB][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10089487	TM2D2	cis	cerebellum	SCAN
rs10089487	TM2D2	cis	Muscle Skeletal	GTEx
rs10089487	ADAM32	cis	parietal	SCAN
rs10089487	SGK196	cis	parietal	SCAN
rs10089487	ADAM32	cis	cerebellum	SCAN
rs10089487	DDHD2	cis	cerebellum	SCAN
rs10089487	TM2D2	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:38855200-38864600	Weak transcription	Spleen	Spleen
2	chr8:38855800-38881600	Weak transcription	Fetal Kidney	kidney
3	chr8:38856600-38860400	Weak transcription	Gastric	stomach
4	chr8:38856600-38861800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:38856600-38889600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr8:38856800-38858600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr8:38856800-38859000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr8:38856800-38859400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr8:38856800-38859600	Weak transcription	Primary B cells from cord blood	blood
10	chr8:38856800-38860200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr8:38856800-38862000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:38856800-38862200	Weak transcription	Aorta	Aorta
13	chr8:38856800-38862400	Weak transcription	Brain Hippocampus Middle	brain
14	chr8:38856800-38865600	Weak transcription	Dnd41	blood
15	chr8:38856800-38866600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr8:38856800-38866600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr8:38856800-38869400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr8:38856800-38869400	Weak transcription	Liver	Liver
19	chr8:38856800-38874400	Weak transcription	Brain Anterior Caudate	brain
20	chr8:38856800-38889600	Weak transcription	Colonic Mucosa	Colon
21	chr8:38857000-38858800	Enhancers	Fetal Heart	heart
22	chr8:38857000-38859000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr8:38857200-38858800	Enhancers	Small Intestine	intestine
24	chr8:38857200-38859000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr8:38857200-38859200	Enhancers	Colon Smooth Muscle	Colon
26	chr8:38857200-38859200	Enhancers	Stomach Mucosa	stomach
27	chr8:38857200-38859800	Flanking Active TSS	HUVEC	blood vessel
28	chr8:38857200-38881400	Weak transcription	Fetal Brain Female	brain
29	chr8:38857400-38858600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr8:38857400-38858600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr8:38857400-38858600	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr8:38857400-38859200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr8:38857400-38859200	Enhancers	Fetal Lung	lung
34	chr8:38857400-38861000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr8:38857400-38865600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr8:38857400-38872400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr8:38857600-38858800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr8:38857600-38858800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr8:38857600-38858800	Enhancers	K562	blood
40	chr8:38857600-38859000	Enhancers	HMEC	breast
41	chr8:38857600-38859200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr8:38857600-38859600	Enhancers	GM12878-XiMat	blood
43	chr8:38857600-38860200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr8:38857600-38861600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr8:38857600-38861600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr8:38857600-38862000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr8:38857600-38864400	Weak transcription	Brain Substantia Nigra	brain
48	chr8:38857600-38866400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr8:38857600-38869200	Weak transcription	Brain Angular Gyrus	brain
50	chr8:38857600-38872200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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