Variant report

Variant	rs3008647
Chromosome Location	chr1:222759007-222759008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222759001..222761767-chr1:222763501..222765317,2	MCF-7	breast:
2	chr1:222755495..222757533-chr1:222758954..222760766,2	K562	blood:
3	chr1:222731700..222734250-chr1:222758511..222761201,3	K562	blood:
4	chr1:222748011..222750721-chr1:222758316..222760837,2	MCF-7	breast:
5	chr1:222757935..222759839-chr1:222790959..222792467,2	K562	blood:
6	chr1:222752431..222755203-chr1:222757791..222760402,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1024065	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10495194	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17463740	0.92[EUR][1000 genomes]
rs17464857	0.81[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17511318	0.81[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1909194	1.00[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1982983	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2006790	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936030	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936039	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936041	0.80[ASW][hapmap];0.81[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936044	0.85[EUR][1000 genomes]
rs2936045	0.85[EUR][1000 genomes]
rs2936046	0.85[EUR][1000 genomes]
rs3002130	1.00[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3008645	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3008653	0.83[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008654	0.81[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3008655	0.84[EUR][1000 genomes]
rs35750438	0.92[EUR][1000 genomes]
rs3748625	0.97[ASN][1000 genomes]
rs3828060	0.97[ASN][1000 genomes]
rs4328077	0.90[EUR][1000 genomes]
rs73122816	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73122823	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73122834	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73122837	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73122849	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73122850	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73122857	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74145503	0.91[AMR][1000 genomes]
rs74148133	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74148140	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74148142	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9441828	0.81[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs9441911	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873203	chr1:222332906-222775000	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1842070	chr1:222732027-222763235	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222721200-222762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:222721800-222762400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:222725600-222762200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:222727600-222762600	Weak transcription	Aorta	Aorta
5	chr1:222727800-222762400	Weak transcription	Thymus	Thymus
6	chr1:222728200-222762200	Weak transcription	Small Intestine	intestine
7	chr1:222729600-222762400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:222730800-222760200	Weak transcription	Brain Substantia Nigra	brain
9	chr1:222730800-222761200	Weak transcription	Fetal Brain Male	brain
10	chr1:222731200-222762400	Weak transcription	Spleen	Spleen
11	chr1:222731600-222762200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:222733600-222762400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:222733800-222761800	Weak transcription	Brain Angular Gyrus	brain
14	chr1:222733800-222762200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:222734000-222762400	Weak transcription	Right Ventricle	heart
16	chr1:222734200-222762400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:222734800-222762200	Weak transcription	Colonic Mucosa	Colon
18	chr1:222739000-222761600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:222742200-222762400	Weak transcription	Fetal Kidney	kidney
20	chr1:222742800-222759600	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:222742800-222760200	Weak transcription	Psoas Muscle	Psoas
22	chr1:222742800-222762200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:222743000-222762400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:222743400-222759400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:222743400-222761600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:222743600-222762200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:222744600-222759600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:222745200-222759600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:222745800-222762200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:222746000-222762600	Weak transcription	Lung	lung
31	chr1:222746600-222761800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:222749800-222759400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:222750400-222762000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:222751000-222760200	Weak transcription	Adipose Nuclei	Adipose
35	chr1:222751000-222761600	Weak transcription	Brain Germinal Matrix	brain
36	chr1:222751000-222762600	Weak transcription	Left Ventricle	heart
37	chr1:222751600-222762200	Weak transcription	Fetal Heart	heart
38	chr1:222752000-222759400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:222754600-222759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:222754600-222760800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:222754600-222761800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:222754800-222761200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:222754800-222761400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:222754800-222761600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:222754800-222761800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:222756000-222761800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:222756000-222762200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:222756000-222762200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:222756200-222761800	Weak transcription	NHLF	lung
50	chr1:222756200-222762200	Weak transcription	Primary hematopoietic stem cells	blood

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