Variant report

Variant	rs11183229
Chromosome Location	chr12:46289948-46289949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46271607..46274125-chr12:46289637..46291918,2	K562	blood:
2	chr12:46288613..46290227-chr12:46314013..46316136,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCAF11-4	chr12:46288603-46290522	NONHSAT027840

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10161306	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.85[ASN][1000 genomes]
rs1062905	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10880873	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10880874	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10880883	0.82[ASN][1000 genomes]
rs11183185	0.82[AFR][1000 genomes]
rs11183191	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11183192	0.88[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs11183208	0.90[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11183210	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11183217	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11183223	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11183226	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183228	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183234	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11183251	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183272	0.85[JPT][hapmap]
rs11183273	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.85[ASN][1000 genomes]
rs11183275	0.82[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs11574964	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12318248	0.85[ASN][1000 genomes]
rs1366024	0.82[JPT][hapmap]
rs1427750	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs17096308	0.81[ASN][1000 genomes]
rs17096361	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1896539	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.81[ASN][1000 genomes]
rs2408437	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3815661	0.82[AFR][1000 genomes]
rs4144983	0.84[ASN][1000 genomes]
rs4768098	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4768099	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4768100	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768667	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768670	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768672	0.85[ASN][1000 genomes]
rs56146240	0.81[AMR][1000 genomes]
rs56176440	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61924070	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61925812	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67136007	0.85[ASN][1000 genomes]
rs735351	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[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	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	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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46245400-46318600	Weak transcription	Small Intestine	intestine
2	chr12:46259000-46316600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:46269000-46319200	Weak transcription	Spleen	Spleen
4	chr12:46269400-46316200	Weak transcription	Brain Angular Gyrus	brain
5	chr12:46269800-46315800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:46273400-46307600	Weak transcription	NHLF	lung
7	chr12:46273400-46310200	Weak transcription	Stomach Mucosa	stomach
8	chr12:46273400-46311200	Weak transcription	Right Ventricle	heart
9	chr12:46273400-46314400	Weak transcription	Brain Substantia Nigra	brain
10	chr12:46275200-46290000	Weak transcription	Fetal Brain Male	brain
11	chr12:46277800-46292400	Strong transcription	Dnd41	blood
12	chr12:46280200-46290000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:46280200-46303400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:46280600-46300800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:46280800-46295400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:46281400-46328800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:46285000-46292200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:46285000-46292200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr12:46285000-46292200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:46285000-46292200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr12:46285000-46292400	Strong transcription	Liver	Liver
22	chr12:46285000-46295800	Strong transcription	Fetal Thymus	thymus
23	chr12:46285400-46291400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr12:46285400-46292200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:46285400-46292200	Strong transcription	Placenta	Placenta
26	chr12:46285400-46292600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:46285400-46292600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:46285400-46292600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:46285400-46293000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr12:46285400-46295800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:46285600-46290200	Strong transcription	Brain Cingulate Gyrus	brain
32	chr12:46285600-46290400	Strong transcription	HSMMtube	muscle
33	chr12:46285600-46290600	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:46285600-46290600	Strong transcription	HepG2	liver
35	chr12:46285600-46291000	Strong transcription	Fetal Intestine Large	intestine
36	chr12:46285600-46291000	Strong transcription	Fetal Muscle Leg	muscle
37	chr12:46285600-46291200	Strong transcription	Adipose Nuclei	Adipose
38	chr12:46285600-46291400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:46285600-46291600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:46285600-46291600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:46285600-46291600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr12:46285600-46291800	Strong transcription	A549	lung
43	chr12:46285600-46292000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:46285600-46292000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:46285600-46292000	Strong transcription	Left Ventricle	heart
46	chr12:46285600-46292200	Strong transcription	HSMM	muscle
47	chr12:46285600-46292400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:46285600-46292400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr12:46285600-46292400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:46285600-46295800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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