Variant report

Variant	rs247920
Chromosome Location	chr12:46268766-46268767
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1012642	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10748432	0.95[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10785593	0.85[ASN][1000 genomes]
rs10880855	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs10880859	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10880860	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10880864	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10880871	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]
rs10880875	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10880879	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10880880	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10880884	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11183201	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11183210	0.81[JPT][hapmap]
rs11183241	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183243	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183268	0.85[ASN][1000 genomes]
rs11183272	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12314770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12319077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12320533	0.81[ASN][1000 genomes]
rs1366024	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468993	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1650008	0.84[EUR][1000 genomes]
rs1863127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2059404	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2193749	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs2408435	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs247917	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247918	0.87[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247919	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247929	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247930	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35121	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35122	0.93[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35125	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582574	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7132422	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7138997	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs724909	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7298703	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7306229	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7315731	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7955891	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7967208	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7970129	0.83[ASN][1000 genomes]
rs7971993	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7976870	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs997307	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[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	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	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv558782	chr12:46254995-46286683	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46242200-46272000	Weak transcription	Stomach Mucosa	stomach
2	chr12:46245400-46272800	Weak transcription	NHDF-Ad	bronchial
3	chr12:46245400-46318600	Weak transcription	Small Intestine	intestine
4	chr12:46245800-46271000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:46245800-46271600	Weak transcription	HUVEC	blood vessel
6	chr12:46245800-46272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:46246000-46272600	Weak transcription	Fetal Heart	heart
8	chr12:46246000-46285400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr12:46246600-46274800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:46246600-46285400	Weak transcription	NH-A	brain
11	chr12:46246600-46285600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:46246600-46286000	Weak transcription	HMEC	breast
13	chr12:46246800-46269000	Weak transcription	Osteobl	bone
14	chr12:46246800-46288000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:46248000-46271000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:46248000-46272600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:46248000-46275400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:46248000-46279400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:46248000-46279600	Weak transcription	Gastric	stomach
20	chr12:46249800-46273000	Weak transcription	Psoas Muscle	Psoas
21	chr12:46251800-46283400	Strong transcription	Fetal Thymus	thymus
22	chr12:46252400-46277400	Strong transcription	Dnd41	blood
23	chr12:46254800-46278600	Weak transcription	NHEK	skin
24	chr12:46257200-46270200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:46259000-46316600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:46259200-46270800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:46261600-46269600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:46262200-46278400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:46265200-46268800	Strong transcription	Primary B cells from cord blood	blood
30	chr12:46265400-46269800	Strong transcription	Placenta	Placenta
31	chr12:46265600-46269000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:46265600-46271200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:46265800-46270000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:46266000-46269600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:46266000-46271400	Strong transcription	Primary T cells from cord blood	blood
36	chr12:46266200-46268800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:46266200-46268800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:46266200-46269000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:46266200-46269400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:46266200-46269600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:46266200-46269600	Strong transcription	GM12878-XiMat	blood
42	chr12:46266200-46269800	Strong transcription	Adipose Nuclei	Adipose
43	chr12:46266200-46269800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr12:46266200-46270000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr12:46266200-46270000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:46266200-46270000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:46266200-46270200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:46266200-46270400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:46266200-46270600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr12:46266200-46270800	Strong transcription	Rectal Mucosa Donor 29	rectum

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