Variant report

Variant	rs2373689
Chromosome Location	chr2:39987287-39987288
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	chr2:39986915..39988908-chr2:40004711..40006490,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10164984	0.83[EUR][1000 genomes]
rs10174709	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10206408	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10207589	1.00[CEU][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10211306	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1035138	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1035139	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11124691	0.86[ASN][1000 genomes]
rs11124692	0.87[EUR][1000 genomes]
rs11124693	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11684302	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12470473	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12617624	0.84[ASN][1000 genomes]
rs12620957	0.84[ASN][1000 genomes]
rs12623462	0.88[ASN][1000 genomes]
rs12623545	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12624217	0.88[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12712653	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12712656	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs13026313	0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13400213	0.83[EUR][1000 genomes]
rs13425906	0.87[ASN][1000 genomes]
rs13428837	0.83[EUR][1000 genomes]
rs1548877	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17478972	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1861243	0.83[EUR][1000 genomes]
rs1861258	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1986876	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2041735	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2058620	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2110656	0.88[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2192685	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs2241115	0.83[JPT][hapmap]
rs2540226	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2540227	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2540228	0.85[EUR][1000 genomes]
rs2716727	0.82[ASN][1000 genomes]
rs2716729	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2716730	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35761077	0.88[ASN][1000 genomes]
rs3732121	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732122	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4670955	0.87[ASN][1000 genomes]
rs4670956	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4670957	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670958	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670959	0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59756273	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6544242	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6719179	0.92[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6722610	1.00[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6731026	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6731450	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6747842	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6750252	0.91[ASN][1000 genomes]
rs6758453	0.93[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs727376	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7560642	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7565954	0.80[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs7581406	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7590912	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]
rs7591296	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7591347	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8265	0.89[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs917960	0.84[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs917962	0.84[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs917963	0.80[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs9309042	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs962262	0.81[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs997976	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2373689	TMEM178	cis	cerebellum	SCAN
rs2373689	CCDC75	cis	parietal	SCAN
rs2373689	THUMPD2	cis	cerebellum	SCAN
rs2373689	CYP1B1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39962200-39993200	Strong transcription	Liver	Liver
2	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:39967600-39991200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
7	chr2:39971600-39998800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:39972400-39998600	Strong transcription	HMEC	breast
9	chr2:39972400-39998800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr2:39973000-39998800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:39974200-39998600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:39974600-39994000	Strong transcription	Fetal Thymus	thymus
13	chr2:39975000-39998400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:39975000-39999800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:39975200-39987400	Strong transcription	Fetal Lung	lung
16	chr2:39975200-39987400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr2:39975200-39989000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr2:39975200-39989800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:39975200-39993800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:39975400-39987800	Strong transcription	Fetal Intestine Large	intestine
21	chr2:39975400-39997000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:39975800-39989400	Strong transcription	A549	lung
23	chr2:39975800-39994600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:39976000-39988600	Strong transcription	HepG2	liver
25	chr2:39976000-39988800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr2:39976000-39989800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:39976000-39993200	Strong transcription	Placenta	Placenta
28	chr2:39976000-39993400	Strong transcription	Adipose Nuclei	Adipose
29	chr2:39976200-39987800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr2:39976200-39987800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:39976200-39995400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:39976200-39998800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:39976400-39992000	Strong transcription	K562	blood
34	chr2:39976600-39992000	Strong transcription	Primary B cells from cord blood	blood
35	chr2:39976800-39987600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr2:39976800-39988800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:39976800-39999000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:39977000-39987600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:39977000-39990000	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:39977200-39988000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:39977200-39989000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:39978200-39988600	Strong transcription	GM12878-XiMat	blood
43	chr2:39978600-40000000	Weak transcription	Fetal Heart	heart
44	chr2:39979800-39989200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:39980000-39987400	Strong transcription	Left Ventricle	heart
46	chr2:39980000-39992000	Strong transcription	Primary T cells from cord blood	blood
47	chr2:39980400-39988200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:39980400-39989400	Strong transcription	HSMMtube	muscle
49	chr2:39981000-39988000	Strong transcription	HUVEC	blood vessel
50	chr2:39981000-39988200	Strong transcription	Dnd41	blood

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