Variant report

Variant	rs12572911
Chromosome Location	chr10:6449962-6449963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6243567..6245351-chr10:6449520..6452478,2	K562	blood:
2	chr10:6240172..6247565-chr10:6441706..6450964,34	MCF-7	breast:
3	chr10:6437383..6440179-chr10:6448797..6450334,2	MCF-7	breast:
4	chr10:6447268..6450081-chr10:6450323..6453408,3	K562	blood:
5	chr10:6241662..6248347-chr10:6438932..6450669,77	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213994	Chromatin interaction
ENSG00000170525	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10508308	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs10752329	0.90[ASN][1000 genomes]
rs10752330	0.90[ASN][1000 genomes]
rs10906429	0.86[ASW][hapmap];1.00[YRI][hapmap]
rs10906504	0.90[ASN][1000 genomes]
rs11258500	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11258501	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11258515	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11258589	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11258612	0.92[ASN][1000 genomes]
rs17155850	0.85[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs17155855	0.85[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2296125	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34316142	0.90[ASN][1000 genomes]
rs35935618	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3793725	0.85[CEU][hapmap]
rs3793726	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs4237436	0.90[ASN][1000 genomes]
rs4750422	0.90[ASN][1000 genomes]
rs590467	0.85[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs681071	0.88[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs681604	0.88[TSI][hapmap]
rs686333	0.90[ASN][1000 genomes]
rs688853	0.85[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs71479777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898408	0.90[ASN][1000 genomes]
rs7918923	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs961203	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[ASN][1000 genomes]
rs9633784	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3357360	chr10:6447346-6451644	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6443400-6452000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:6443800-6451800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:6444000-6451200	Weak transcription	Aorta	Aorta
4	chr10:6444000-6451400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:6444000-6451600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr10:6444000-6452000	Weak transcription	Brain Anterior Caudate	brain
7	chr10:6444000-6452000	Weak transcription	Right Ventricle	heart
8	chr10:6444000-6452400	Weak transcription	Right Atrium	heart
9	chr10:6444200-6452000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:6445200-6451000	Weak transcription	Dnd41	blood
11	chr10:6445600-6450800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr10:6445600-6452000	Weak transcription	Psoas Muscle	Psoas
13	chr10:6446000-6452000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:6448800-6451400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr10:6449000-6451200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr10:6449000-6451600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr10:6449200-6450600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr10:6449200-6450800	Weak transcription	Thymus	Thymus
19	chr10:6449200-6451200	Weak transcription	Fetal Thymus	thymus
20	chr10:6449200-6451600	Weak transcription	Primary T cells from cord blood	blood
21	chr10:6449200-6451800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr10:6449200-6451800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr10:6449200-6451800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr10:6449400-6451000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr10:6449400-6451600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr10:6449600-6450800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr10:6449600-6451400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr10:6449600-6452000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr10:6449600-6452600	Weak transcription	Pancreas	Pancrea
30	chr10:6449800-6450800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr10:6449800-6451800	Weak transcription	Fetal Kidney	kidney

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