Variant report

Variant	rs17721302
Chromosome Location	chr1:212435062-212435063
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212433580..212437066-chr1:212438671..212444004,6	K562	blood:
2	chr1:212434393..212437066-chr1:212439092..212441986,2	K562	blood:
3	chr1:212433329..212435940-chr1:212436148..212437997,2	K562	blood:
4	chr1:212432994..212436361-chr1:212456253..212459634,4	K562	blood:
5	chr1:212428875..212432292-chr1:212434801..212437724,6	K562	blood:
6	chr1:211770787..211772402-chr1:212434054..212436587,2	K562	blood:
7	chr1:212427899..212432292-chr1:212432529..212438731,7	K562	blood:
8	chr1:212404851..212407731-chr1:212434475..212437929,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10494951	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10863960	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863961	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10863963	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11119899	0.98[ASN][1000 genomes]
rs11119919	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11119920	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11119924	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11119930	1.00[CHB][hapmap]
rs11576437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11579999	0.88[ASN][1000 genomes]
rs11580285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585215	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11587555	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11588867	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11589817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11590242	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11590672	0.95[CEU][hapmap];0.89[CHB][hapmap]
rs12060029	1.00[CHB][hapmap]
rs12064553	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12066356	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12722832	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726409	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12727947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12730098	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12736502	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12737825	0.80[AFR][1000 genomes]
rs12743785	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12745269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12746203	0.90[AFR][1000 genomes]
rs12747025	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756678	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1470390	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1493600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1530451	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2120770	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2297306	1.00[CHB][hapmap]
rs2358448	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2358454	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs34212128	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34244392	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34447409	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34740542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35872305	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55814152	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6661987	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6667199	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6693849	1.00[YRI][hapmap]
rs71646153	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7518399	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7521041	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7531219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs968531	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs968532	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17721302	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs17721302	RP11-15I11.3	cis	lung	GTEx
rs17721302	RP11-15I11.3	cis	Nerve Tibial	GTEx
rs17721302	RP11-15I11.3	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212429400-212435600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:212430400-212435600	Enhancers	HepG2	liver
3	chr1:212433200-212435600	Enhancers	HMEC	breast
4	chr1:212433600-212435200	Enhancers	Liver	Liver
5	chr1:212433600-212435400	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr1:212433600-212435800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:212433800-212435200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:212433800-212435200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:212433800-212435600	Enhancers	Hela-S3	cervix
10	chr1:212434000-212435400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:212434000-212435400	Enhancers	Stomach Mucosa	stomach
12	chr1:212434000-212435600	Enhancers	Fetal Intestine Small	intestine
13	chr1:212434000-212435800	Enhancers	Fetal Intestine Large	intestine
14	chr1:212434000-212435800	Enhancers	K562	blood
15	chr1:212434200-212435200	Enhancers	Duodenum Mucosa	Duodenum
16	chr1:212434200-212435600	Enhancers	Primary T cells from cord blood	blood
17	chr1:212434400-212435200	Enhancers	Right Atrium	heart
18	chr1:212434400-212435400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr1:212434400-212435600	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr1:212434400-212436000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr1:212434600-212435200	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr1:212434800-212435200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:212435000-212435400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:212435000-212435600	Enhancers	NHEK	skin

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