Variant report

Variant	rs10840649
Chromosome Location	chr12:122032660-122032661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10770191	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12320939	1.00[CEU][hapmap]
rs2669163	0.96[CEU][hapmap]
rs2669166	0.84[CEU][hapmap]
rs2669168	0.96[CEU][hapmap]
rs2720022	0.96[CEU][hapmap]
rs28409019	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28651135	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28679490	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28758358	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2942368	0.92[CEU][hapmap]
rs2942379	0.84[CEU][hapmap]
rs3825175	0.96[CEU][hapmap]
rs3934658	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7135617	0.84[CEU][hapmap]
rs7300349	0.91[EUR][1000 genomes]
rs7397776	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7398628	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7399127	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122020800-122040400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:122021200-122036000	Weak transcription	Brain Germinal Matrix	brain
3	chr12:122021600-122033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:122028200-122038800	Weak transcription	Pancreas	Pancrea
5	chr12:122028600-122048000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:122028600-122048400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:122028800-122033600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:122028800-122036000	Weak transcription	Fetal Intestine Small	intestine
9	chr12:122028800-122048400	Weak transcription	Brain Angular Gyrus	brain
10	chr12:122028800-122049000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:122028800-122064000	Weak transcription	Right Atrium	heart
12	chr12:122029000-122033400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:122029200-122032800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:122029200-122032800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:122029200-122032800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:122029200-122032800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:122029200-122033600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:122029200-122033600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:122029200-122033600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:122029200-122033600	Weak transcription	K562	blood
21	chr12:122029200-122033800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:122029200-122034600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:122029200-122036200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:122029200-122036600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:122029200-122038000	Weak transcription	NHLF	lung
26	chr12:122029200-122038200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:122029200-122038800	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:122029200-122038800	Weak transcription	HSMMtube	muscle
29	chr12:122029200-122049800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:122029400-122033600	Weak transcription	Dnd41	blood
31	chr12:122029400-122035600	Weak transcription	Fetal Stomach	stomach
32	chr12:122029400-122035800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:122029400-122037000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:122029800-122036400	Weak transcription	Fetal Brain Female	brain
35	chr12:122030200-122037200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:122030400-122034000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:122030400-122036400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:122030600-122033800	Weak transcription	Thymus	Thymus
39	chr12:122030600-122035600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:122030600-122036600	Weak transcription	Primary T cells from cord blood	blood
41	chr12:122030600-122036600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr12:122030600-122036600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:122030600-122039000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:122030800-122036600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:122030800-122036800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:122030800-122037200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:122031200-122038600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:122031600-122035800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:122031800-122033400	Weak transcription	Placenta	Placenta
50	chr12:122031800-122034600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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