Variant report

Variant	rs12302189
Chromosome Location	chr12:121199329-121199330
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	chr1:45186381..45189343-chr12:121198720..121200674,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPPL3.1-1	chr12:121199194-121199395	ENSG00000255946.1

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10431373	0.83[EUR][1000 genomes]
rs10437837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10774570	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10849783	1.00[ASN][1000 genomes]
rs10849785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10849794	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10849795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10849796	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10849798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10849799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10849808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10849809	0.83[EUR][1000 genomes]
rs10849814	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11065242	0.82[JPT][hapmap]
rs11065262	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs11065266	0.90[ASN][1000 genomes]
rs11065271	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11065276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12423697	0.81[ASN][1000 genomes]
rs2229534	0.81[JPT][hapmap]
rs2948150	1.00[CEU][hapmap]
rs3213569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs56137011	0.81[ASN][1000 genomes]
rs73224306	0.80[AMR][1000 genomes]
rs73229135	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1041153	chr12:121171986-121208826	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121194000-121200800	Weak transcription	HepG2	liver
2	chr12:121194200-121202200	Weak transcription	K562	blood
3	chr12:121195000-121201200	Weak transcription	Small Intestine	intestine
4	chr12:121195200-121200000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:121195600-121204200	Weak transcription	Stomach Mucosa	stomach
6	chr12:121195600-121207200	Strong transcription	Brain Germinal Matrix	brain
7	chr12:121196000-121201000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:121196200-121199400	Weak transcription	Aorta	Aorta
9	chr12:121196200-121201000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:121196200-121201000	Weak transcription	Osteobl	bone
11	chr12:121196400-121207000	Strong transcription	Fetal Brain Female	brain
12	chr12:121196800-121200200	Enhancers	Psoas Muscle	Psoas
13	chr12:121196800-121201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:121196800-121203000	Strong transcription	Fetal Intestine Large	intestine
15	chr12:121196800-121212800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:121197000-121199400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:121197000-121200200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:121197000-121203000	Strong transcription	Fetal Intestine Small	intestine
19	chr12:121197000-121207200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:121197200-121200800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:121197200-121201200	Weak transcription	Ovary	ovary
22	chr12:121197200-121204200	Weak transcription	Fetal Brain Male	brain
23	chr12:121197200-121210000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:121197400-121200200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr12:121197400-121201000	Genic enhancers	Fetal Thymus	thymus
26	chr12:121197400-121201200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:121197400-121203000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr12:121197400-121203400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:121197400-121203400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:121197400-121203800	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:121197400-121207000	Strong transcription	Pancreas	Pancrea
32	chr12:121197400-121209800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:121197400-121212600	Strong transcription	Thymus	Thymus
34	chr12:121197400-121220000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr12:121197600-121199600	Genic enhancers	Spleen	Spleen
36	chr12:121197600-121203000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr12:121197600-121204400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:121197600-121205400	Strong transcription	GM12878-XiMat	blood
39	chr12:121197600-121207200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:121197600-121210400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:121197800-121199400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:121197800-121199400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:121197800-121199400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
44	chr12:121197800-121199600	Genic enhancers	Lung	lung
45	chr12:121197800-121199800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:121197800-121200000	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr12:121197800-121200000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr12:121197800-121201000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:121197800-121203400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr12:121197800-121209000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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