Variant report

Variant	rs924169
Chromosome Location	chr12:62864248-62864249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62859623..62861378-chr12:62862535..62864580,2	K562	blood:
2	chr12:62863210..62865017-chr12:62887916..62890399,2	K562	blood:
3	chr12:62863411..62864986-chr12:62871030..62872716,2	MCF-7	breast:
4	chr12:62829632..62831889-chr12:62864077..62865718,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000061987	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10735906	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747964	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747967	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784297	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784300	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784301	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784304	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877850	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877854	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877871	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11615669	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11832508	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12298863	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498714	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1603823	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029938	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2132648	0.89[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4025987	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763022	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763023	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763171	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581450	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132677	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132765	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133906	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135044	0.95[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135893	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136794	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7298046	0.88[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7303357	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7954432	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7963346	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7963544	0.91[CEU][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964563	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7968424	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7978740	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62861600-62864800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:62861600-62865800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:62861600-62866600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:62861800-62864600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr12:62861800-62864800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr12:62861800-62865000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:62861800-62879800	Weak transcription	HSMMtube	muscle
8	chr12:62861800-62902200	Weak transcription	Fetal Kidney	kidney
9	chr12:62862200-62864400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:62862200-62864600	Enhancers	Liver	Liver
11	chr12:62862800-62867200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:62862800-62895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:62863000-62864400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:62863000-62869400	Weak transcription	Fetal Intestine Small	intestine
15	chr12:62863200-62864400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:62863200-62864400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:62863200-62864400	Weak transcription	HSMM	muscle
18	chr12:62863200-62864600	Enhancers	Adipose Nuclei	Adipose
19	chr12:62863200-62864800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr12:62863200-62864800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:62863200-62864800	Weak transcription	Fetal Thymus	thymus
22	chr12:62863200-62865000	Weak transcription	Fetal Stomach	stomach
23	chr12:62863200-62865000	Weak transcription	Left Ventricle	heart
24	chr12:62863200-62865600	Weak transcription	Right Ventricle	heart
25	chr12:62863200-62865800	Weak transcription	Aorta	Aorta
26	chr12:62863200-62866000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:62863200-62866000	Weak transcription	NHLF	lung
28	chr12:62863200-62866200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:62863200-62866200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:62863200-62870400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:62863200-62870600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:62863200-62870600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:62863200-62871000	Weak transcription	Placenta	Placenta
34	chr12:62863200-62871000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:62863200-62871200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:62863200-62875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:62863200-62875600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:62863200-62875600	Weak transcription	Gastric	stomach
39	chr12:62863200-62876000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:62863200-62879400	Weak transcription	Thymus	Thymus
41	chr12:62863200-62881400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:62863200-62895200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr12:62863200-62896800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr12:62863200-62901800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:62863200-62937400	Weak transcription	Pancreas	Pancrea
46	chr12:62863400-62864400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:62863400-62864400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:62863400-62864400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:62863400-62864400	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr12:62863400-62864600	Enhancers	Brain Hippocampus Middle	brain

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