Variant report

Variant	rs7565954
Chromosome Location	chr2:39950482-39950483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39941387..39944301-chr2:39949793..39952707,2	MCF-7	breast:
2	chr2:39664058..39665655-chr2:39949878..39951960,2	MCF-7	breast:
3	chr2:39949939..39952717-chr2:39956510..39959520,3	K562	blood:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10206408	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11124691	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12470473	0.90[CHD][hapmap];0.83[JPT][hapmap]
rs12617624	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12623462	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12623545	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12624217	0.87[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap]
rs12712653	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs13026313	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs13401182	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13425906	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1978327	0.80[EUR][1000 genomes]
rs1986876	0.93[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2041735	0.83[ASN][1000 genomes]
rs2058620	0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2110656	0.93[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs2160198	0.91[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2160199	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs2192685	0.83[GIH][hapmap];0.80[MEX][hapmap]
rs2215958	0.85[EUR][1000 genomes]
rs2373688	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2373689	0.80[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs2540226	0.89[ASN][1000 genomes]
rs2540227	0.84[ASN][1000 genomes]
rs2540229	0.83[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2716704	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2716727	0.92[ASN][1000 genomes]
rs2716729	0.84[ASN][1000 genomes]
rs2716730	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3732121	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs3732122	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3902124	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4365444	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4644998	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4670955	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4670956	0.93[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4670957	0.93[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4670958	0.91[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4670959	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs6544242	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6719179	0.91[ASW][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6731026	0.81[ASN][1000 genomes]
rs6731450	0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs6747842	0.87[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs6750252	0.84[ASN][1000 genomes]
rs6758453	0.87[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs7560642	0.87[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs7581406	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7591296	0.86[ASN][1000 genomes]
rs7591347	0.86[ASN][1000 genomes]
rs917960	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs917962	0.93[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs917963	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs962262	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs997976	0.87[CHB][hapmap];0.88[JPT][hapmap]

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	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7565954	MAP4K3	cis	lung	GTEx
rs7565954	THUMPD2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39925000-39957600	Weak transcription	Fetal Stomach	stomach
2	chr2:39931400-39957600	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:39936600-39950600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:39938000-39957600	Weak transcription	Fetal Brain Female	brain
5	chr2:39938200-39950600	Weak transcription	HSMMtube	muscle
6	chr2:39940800-39950800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:39942000-39963000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:39943200-39956200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
10	chr2:39945200-39954400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:39946400-39950600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:39946600-39951200	Weak transcription	Aorta	Aorta
13	chr2:39946800-39950600	Weak transcription	Osteobl	bone
14	chr2:39946800-39959600	Weak transcription	Brain Germinal Matrix	brain
15	chr2:39947800-39959800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:39948200-39961200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:39948400-39950800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:39948600-39950800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:39948600-39950800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:39948600-39950800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:39948800-39952400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:39948800-39959600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:39949000-39950800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:39949000-39950800	Enhancers	Fetal Heart	heart
25	chr2:39949000-39951000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:39949000-39951000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:39949000-39952400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:39949000-39960400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:39949800-39950600	Enhancers	Psoas Muscle	Psoas
30	chr2:39949800-39952200	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:39950000-39951000	Enhancers	Left Ventricle	heart
32	chr2:39950000-39953400	Enhancers	NH-A	brain
33	chr2:39950000-39954400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:39950200-39952400	Enhancers	Skeletal Muscle Male	skeletal muscle

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