Variant report

Variant	rs10880871
Chromosome Location	chr12:46340738-46340739
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46338501..46342141-chr12:46348337..46351677,3	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1012642	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10748432	0.95[CEU][hapmap]
rs10748438	0.83[YRI][hapmap]
rs10785593	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10880855	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs10880864	0.84[EUR][1000 genomes]
rs10880875	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880879	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11183201	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs11183241	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183268	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11574952	0.85[YRI][hapmap]
rs12314770	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12319077	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1366024	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468993	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1650008	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17096380	0.85[YRI][hapmap]
rs1863127	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2059404	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2408435	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs247917	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs247918	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs247919	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247920	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247929	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs247930	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35115	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35121	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35122	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35125	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6582574	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs7132422	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs724909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298703	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966125	0.80[ASN][1000 genomes]
rs7967208	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970129	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7971993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7976870	0.96[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7979218	1.00[YRI][hapmap]
rs997307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv3439887	chr12:46337377-46370366	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46299000-46381000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:46312200-46348600	Strong transcription	Dnd41	blood
3	chr12:46314600-46345600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:46316600-46343400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:46317000-46341400	Weak transcription	Gastric	stomach
6	chr12:46319200-46341400	Weak transcription	Lung	lung
7	chr12:46319200-46362800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:46322600-46341400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:46322600-46341400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:46322600-46341400	Weak transcription	Pancreas	Pancrea
11	chr12:46322600-46360200	Weak transcription	Fetal Brain Male	brain
12	chr12:46323200-46341400	Weak transcription	Colonic Mucosa	Colon
13	chr12:46323200-46341400	Weak transcription	Fetal Stomach	stomach
14	chr12:46323200-46341400	Weak transcription	Spleen	Spleen
15	chr12:46324400-46351600	Weak transcription	Psoas Muscle	Psoas
16	chr12:46325000-46341400	Weak transcription	Left Ventricle	heart
17	chr12:46325200-46343400	Weak transcription	Right Ventricle	heart
18	chr12:46326600-46360400	Weak transcription	Small Intestine	intestine
19	chr12:46328800-46345200	Strong transcription	HSMM	muscle
20	chr12:46329200-46351800	Weak transcription	Fetal Heart	heart
21	chr12:46329400-46344400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:46329600-46341400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:46329600-46342600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:46329600-46348800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:46329800-46371000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:46330400-46344800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr12:46330400-46358800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:46331000-46344600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:46331000-46347000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr12:46331200-46343000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:46331200-46344000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:46331200-46344200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:46331200-46344600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr12:46331200-46344800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:46331400-46343200	Strong transcription	GM12878-XiMat	blood
36	chr12:46331400-46344000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:46331400-46351200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:46331600-46345000	Strong transcription	Placenta	Placenta
39	chr12:46331800-46344000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:46331800-46344200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr12:46332200-46341400	Weak transcription	Ovary	ovary
42	chr12:46332200-46344000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:46333200-46342400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:46333600-46343000	Strong transcription	Fetal Lung	lung
45	chr12:46333600-46344000	Strong transcription	Liver	Liver
46	chr12:46333600-46344800	Strong transcription	Primary B cells from cord blood	blood
47	chr12:46333600-46345200	Strong transcription	Fetal Thymus	thymus
48	chr12:46333600-46345200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr12:46334000-46342600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:46334000-46343000	Strong transcription	Primary T cells from cord blood	blood

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