Variant report

Variant	rs2993541
Chromosome Location	chr1:212109825-212109826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DTL-6	chr1:212109591-212109976	NONHSAT009338

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10779568	0.82[EUR][1000 genomes]
rs10863939	0.82[EUR][1000 genomes]
rs1316820	0.81[ASN][1000 genomes]
rs1578992	0.81[CEU][hapmap];0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1578993	0.84[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs1806360	0.82[EUR][1000 genomes]
rs1933593	0.80[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2014029	0.86[CHB][hapmap]
rs2105162	0.85[ASN][1000 genomes]
rs2248191	0.86[CHB][hapmap]
rs2251398	0.82[EUR][1000 genomes]
rs2358386	0.84[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2788133	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788139	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2788140	0.80[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808385	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2808392	0.81[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2970601	0.81[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2993528	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2993534	0.83[ASN][1000 genomes]
rs2993544	0.80[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3009985	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3010003	0.81[ASN][1000 genomes]
rs3010004	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3010006	0.85[ASN][1000 genomes]
rs3738449	0.80[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs4951435	0.81[ASN][1000 genomes]
rs59706922	0.87[ASN][1000 genomes]
rs6684814	0.87[ASN][1000 genomes]
rs7522330	0.81[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2993541	INTS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212084800-212113000	Weak transcription	Brain Anterior Caudate	brain
2	chr1:212102400-212113200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:212102600-212115200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:212102600-212120400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:212102800-212111400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:212102800-212114400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:212102800-212115000	Weak transcription	Fetal Thymus	thymus
8	chr1:212102800-212115200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:212103000-212132600	Weak transcription	Gastric	stomach
10	chr1:212103200-212115000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:212103200-212115000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:212103200-212115200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:212103200-212115200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:212103400-212111600	Weak transcription	Liver	Liver
15	chr1:212103400-212113200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:212103400-212113200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:212103600-212111800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:212103600-212111800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:212103600-212115000	Weak transcription	NHEK	skin
20	chr1:212103600-212115400	Weak transcription	HMEC	breast
21	chr1:212103600-212132200	Weak transcription	Esophagus	oesophagus
22	chr1:212103800-212132200	Weak transcription	NHLF	lung
23	chr1:212104000-212117600	Weak transcription	HepG2	liver
24	chr1:212104200-212115000	Weak transcription	Lung	lung
25	chr1:212104800-212114800	Weak transcription	Hela-S3	cervix
26	chr1:212104800-212124400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:212106200-212111800	Weak transcription	Primary B cells from cord blood	blood
28	chr1:212106200-212148600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:212106400-212111800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:212106400-212111800	Weak transcription	Left Ventricle	heart
31	chr1:212106400-212115000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:212106400-212132400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:212106400-212132600	Weak transcription	Right Ventricle	heart
34	chr1:212106400-212147800	Weak transcription	NH-A	brain
35	chr1:212106800-212111800	Weak transcription	Adipose Nuclei	Adipose
36	chr1:212106800-212112200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:212106800-212113400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:212107000-212110200	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr1:212107000-212111800	Weak transcription	K562	blood
40	chr1:212107000-212115000	Weak transcription	Placenta	Placenta
41	chr1:212107000-212115200	Weak transcription	HSMM	muscle
42	chr1:212107000-212118000	Weak transcription	HSMMtube	muscle
43	chr1:212107000-212132800	Weak transcription	Pancreas	Pancrea
44	chr1:212107200-212116600	Weak transcription	HUVEC	blood vessel
45	chr1:212107400-212115000	Weak transcription	Fetal Brain Female	brain
46	chr1:212108000-212111800	Weak transcription	Right Atrium	heart
47	chr1:212108000-212115000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:212108000-212132400	Weak transcription	Spleen	Spleen
49	chr1:212108200-212115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:212108400-212115200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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