Variant report

Variant	rs7605939
Chromosome Location	chr2:39649110-39649111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39647976..39656890-chr2:39661783..39666548,15	MCF-7	breast:
2	chr2:39646458..39648689-chr2:39648799..39652101,4	K562	blood:
3	chr2:39643207..39646078-chr2:39648407..39650074,2	K562	blood:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10169501	0.83[ASN][1000 genomes]
rs10173722	0.82[ASN][1000 genomes]
rs10196447	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs10199459	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10199948	0.81[JPT][hapmap]
rs11124683	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11896389	0.91[EUR][1000 genomes]
rs12328714	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12624242	0.88[MKK][hapmap]
rs12712640	0.92[MKK][hapmap]
rs17023530	0.94[EUR][1000 genomes]
rs17023542	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17023547	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs17023600	0.94[EUR][1000 genomes]
rs17023611	0.94[EUR][1000 genomes]
rs17023684	1.00[EUR][1000 genomes]
rs17023696	0.82[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];1.00[EUR][1000 genomes]
rs17023773	0.97[EUR][1000 genomes]
rs17446102	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs17446515	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs17446690	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs17505580	0.94[EUR][1000 genomes]
rs17505877	0.94[EUR][1000 genomes]
rs2056653	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2056655	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2111383	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2373530	0.88[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs2373532	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3732052	1.00[EUR][1000 genomes]
rs4670273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670938	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55761128	1.00[EUR][1000 genomes]
rs6544227	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6544229	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6720537	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6720951	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6721049	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6721740	0.97[EUR][1000 genomes]
rs6731310	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6758596	0.93[ASW][hapmap];1.00[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];0.99[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73924009	1.00[EUR][1000 genomes]
rs7559436	1.00[EUR][1000 genomes]
rs7577097	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7588265	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs7596222	0.88[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs9037	0.84[MKK][hapmap]
rs9309036	0.81[MKK][hapmap]

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	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39636600-39651400	Weak transcription	Fetal Thymus	thymus
2	chr2:39637200-39659000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:39637600-39651400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:39638800-39652400	Weak transcription	Hela-S3	cervix
5	chr2:39639200-39658000	Weak transcription	Fetal Stomach	stomach
6	chr2:39639600-39657200	Weak transcription	HMEC	breast
7	chr2:39640800-39649200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:39640800-39652400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:39640800-39656800	Weak transcription	NH-A	brain
10	chr2:39640800-39660000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:39641000-39651600	Weak transcription	HSMMtube	muscle
12	chr2:39641000-39656600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:39641200-39650200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:39641200-39659600	Weak transcription	Brain Angular Gyrus	brain
15	chr2:39641400-39649200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:39644200-39650000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:39644200-39661600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:39644400-39654200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:39644400-39654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:39644800-39650600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:39645000-39649400	Weak transcription	Dnd41	blood
22	chr2:39645000-39651400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:39645000-39658800	Weak transcription	Brain Anterior Caudate	brain
24	chr2:39645200-39651600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:39645200-39658200	Weak transcription	Right Ventricle	heart
26	chr2:39645400-39651400	Weak transcription	Left Ventricle	heart
27	chr2:39646000-39652400	Weak transcription	Brain Substantia Nigra	brain
28	chr2:39646000-39660200	Weak transcription	Fetal Intestine Small	intestine
29	chr2:39646200-39650400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:39646200-39651600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:39646200-39652000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:39646200-39653200	Weak transcription	Stomach Mucosa	stomach
33	chr2:39646200-39656200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:39646200-39658000	Weak transcription	Liver	Liver
35	chr2:39647000-39657400	Weak transcription	Adipose Nuclei	Adipose
36	chr2:39647200-39649200	Weak transcription	K562	blood
37	chr2:39647200-39651600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:39647200-39652600	Weak transcription	Fetal Heart	heart
39	chr2:39647200-39658400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:39647200-39659000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr2:39647400-39649200	Weak transcription	HepG2	liver
42	chr2:39647400-39650200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:39647400-39650200	Weak transcription	NHLF	lung
44	chr2:39647400-39650400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:39647400-39651600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:39647400-39651600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:39647400-39651600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:39647400-39651600	Weak transcription	A549	lung
49	chr2:39647400-39651600	Weak transcription	HSMM	muscle
50	chr2:39647400-39652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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