Variant report

Variant	rs7590912
Chromosome Location	chr2:39995885-39995886
allele	C/T
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	CTCF	chr2:39995740-39995890	HRE	kidney:	n/a	n/a
2	POLR2A	chr2:39995835-39996275	K562	blood:	n/a	n/a
3	POLR2A	chr2:39995876-39996194	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
THUMPD2	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10164984	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10169390	0.88[ASN][1000 genomes]
rs10174709	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10207589	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10211306	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1035138	0.80[EUR][1000 genomes]
rs1035139	0.80[EUR][1000 genomes]
rs11124692	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11124693	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684302	0.81[CEU][hapmap]
rs12470473	0.84[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs12624217	0.81[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs12712653	0.82[JPT][hapmap]
rs12712656	0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13026313	0.84[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs13400213	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13428837	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1548877	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17478972	0.80[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1861243	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1861258	0.81[CEU][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1986876	0.84[EUR][1000 genomes]
rs2041735	0.92[EUR][1000 genomes]
rs2058620	0.82[JPT][hapmap]
rs2110656	0.83[EUR][1000 genomes]
rs2160199	0.82[CHD][hapmap];0.93[GIH][hapmap]
rs2192685	0.89[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs2241115	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2373689	0.94[ASW][hapmap];0.84[CEU][hapmap];0.80[GIH][hapmap];0.89[LWK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2540226	0.80[EUR][1000 genomes]
rs2540227	0.80[EUR][1000 genomes]
rs2540228	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2540229	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs2716729	0.82[EUR][1000 genomes]
rs2716730	0.80[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs3732121	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3732122	0.84[CEU][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes]
rs3815510	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4670956	0.86[EUR][1000 genomes]
rs4670959	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs59756273	0.93[EUR][1000 genomes]
rs6544242	0.84[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs6719179	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6722610	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6731026	0.86[EUR][1000 genomes]
rs6731450	0.86[EUR][1000 genomes]
rs727376	0.80[EUR][1000 genomes]
rs7560642	0.88[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs7591347	0.84[EUR][1000 genomes]
rs8265	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917961	0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs917962	0.80[GIH][hapmap]
rs9309042	0.80[EUR][1000 genomes]
rs997976	0.84[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7590912	THUMPD2	cis	cerebellum	SCAN
rs7590912	CCDC75	cis	parietal	SCAN
rs7590912	TMEM178	cis	cerebellum	SCAN
rs7590912	CYP1B1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
5	chr2:39971600-39998800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:39972400-39998600	Strong transcription	HMEC	breast
7	chr2:39972400-39998800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:39973000-39998800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:39974200-39998600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:39975000-39998400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:39975000-39999800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:39975400-39997000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:39976200-39998800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:39976800-39999000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:39978600-40000000	Weak transcription	Fetal Heart	heart
16	chr2:39983000-39999200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:39983600-39996400	Strong transcription	NHDF-Ad	bronchial
18	chr2:39983600-39998600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:39983600-39999000	Strong transcription	HSMM	muscle
20	chr2:39984800-39999600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:39985000-39996000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
23	chr2:39985200-39996000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:39985200-39998400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:39985200-39999600	Weak transcription	Brain Germinal Matrix	brain
26	chr2:39985200-39999600	Weak transcription	Psoas Muscle	Psoas
27	chr2:39985200-39999800	Weak transcription	Brain Substantia Nigra	brain
28	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
30	chr2:39985600-40001000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:39985800-39996000	Weak transcription	Esophagus	oesophagus
32	chr2:39985800-39996000	Weak transcription	Gastric	stomach
33	chr2:39985800-39996000	Weak transcription	Pancreas	Pancrea
34	chr2:39985800-39996200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:39985800-39996200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:39985800-39996400	Weak transcription	Fetal Intestine Small	intestine
37	chr2:39985800-39999200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:39985800-39999400	Weak transcription	Aorta	Aorta
39	chr2:39985800-39999600	Weak transcription	Brain Angular Gyrus	brain
40	chr2:39985800-39999800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:39985800-39999800	Weak transcription	Small Intestine	intestine
42	chr2:39985800-40004800	Weak transcription	Fetal Brain Female	brain
43	chr2:39985800-40005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:39985800-40005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:39985800-40005400	Weak transcription	Lung	lung
46	chr2:39986000-39996000	Weak transcription	Fetal Stomach	stomach
47	chr2:39986000-40004200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:39986200-40004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:39986800-39999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:39987400-39999400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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