Variant report

Variant	rs12991346
Chromosome Location	chr2:64168682-64168683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDPCP-6	chr2:64168495-64168884	NONHSAT071081

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10168446	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10199273	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10865343	0.89[CHB][hapmap]
rs10865344	0.92[CEU][hapmap]
rs11125987	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11682249	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.87[ASN][1000 genomes]
rs11692514	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12612549	0.85[CHB][hapmap]
rs13014371	0.90[ASN][1000 genomes]
rs13021953	0.89[ASN][1000 genomes]
rs13023231	0.87[ASN][1000 genomes]
rs13034625	0.90[ASN][1000 genomes]
rs1421093	0.90[ASN][1000 genomes]
rs1440003	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs193031	0.90[YRI][hapmap]
rs329479	0.87[ASN][1000 genomes]
rs329480	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[ASN][1000 genomes]
rs329486	0.80[CHB][hapmap]
rs329489	0.93[ASN][1000 genomes]
rs34506208	0.89[ASN][1000 genomes]
rs34688719	0.91[ASN][1000 genomes]
rs4072113	0.85[CHB][hapmap]
rs4318375	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs4616468	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546031	0.86[ASN][1000 genomes]
rs6546036	0.80[ASN][1000 genomes]
rs6546041	0.90[ASN][1000 genomes]
rs6546043	0.83[CHB][hapmap]
rs6546046	0.85[CHB][hapmap]
rs67247064	0.91[ASN][1000 genomes]
rs6726257	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6758381	0.90[ASN][1000 genomes]
rs6759483	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7596262	0.85[CHB][hapmap]
rs7597935	0.88[CEU][hapmap];0.83[CHB][hapmap]

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	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv521717	chr2:64104132-64186582	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv874236	chr2:64154215-64179235	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1002209	chr2:64160385-64238475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64114000-64212000	Weak transcription	Small Intestine	intestine
2	chr2:64114200-64174800	Weak transcription	Right Ventricle	heart
3	chr2:64129600-64201000	Weak transcription	Hela-S3	cervix
4	chr2:64130400-64211200	Weak transcription	Fetal Brain Male	brain
5	chr2:64130800-64174800	Weak transcription	Stomach Mucosa	stomach
6	chr2:64137400-64204800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:64139000-64172800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:64139800-64220600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:64140400-64187600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:64140400-64188800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:64140600-64172400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:64141200-64187600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:64141400-64189200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:64142800-64189200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:64147600-64178000	Weak transcription	A549	lung
16	chr2:64154400-64176800	Weak transcription	Colonic Mucosa	Colon
17	chr2:64154400-64202600	Weak transcription	Spleen	Spleen
18	chr2:64154600-64174800	Weak transcription	Thymus	Thymus
19	chr2:64154600-64202600	Weak transcription	Pancreas	Pancrea
20	chr2:64154800-64175000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:64154800-64175200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:64154800-64177400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:64154800-64242600	Weak transcription	Aorta	Aorta
24	chr2:64155000-64174800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:64155400-64174200	Weak transcription	Brain Germinal Matrix	brain
26	chr2:64159200-64170000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:64159200-64172400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:64159200-64181400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr2:64159400-64175600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:64159600-64197800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:64159600-64211600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:64159800-64172000	Strong transcription	HepG2	liver
33	chr2:64159800-64172200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr2:64160000-64169800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:64160400-64169000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:64162200-64173200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:64162800-64170400	Weak transcription	Fetal Kidney	kidney
38	chr2:64162800-64183600	Weak transcription	HSMMtube	muscle
39	chr2:64163200-64207600	Weak transcription	HUVEC	blood vessel
40	chr2:64163800-64172400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:64164400-64169200	Strong transcription	Osteobl	bone
42	chr2:64164600-64169200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:64164600-64169200	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:64164600-64169400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:64164800-64171800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:64165000-64169000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:64165200-64168800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:64165600-64175000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:64165600-64177000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:64165600-64193600	Weak transcription	NHLF	lung

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