Variant report

Variant	rs10898954
Chromosome Location	chr11:73790243-73790244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:73789299..73790819-chr11:73795189..73797595,2	K562	blood:
2	chr11:73784249..73785806-chr11:73788589..73790911,2	MCF-7	breast:
3	chr11:73790243..73790743-chr5:138940220..138940886,2	NB4	blood:

Variant related genes	Relation type
ENSG00000131508	Chromatin interaction
ENSG00000168014	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10898956	0.85[ASN][1000 genomes]
rs1614299	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1615115	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1726735	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1726744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1726746	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1726751	0.89[CEU][hapmap]
rs1726752	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1726759	0.87[YRI][hapmap]
rs1726764	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1783537	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1790381	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1790398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790404	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2007567	0.81[ASN][1000 genomes]
rs4453265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474835	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs4944036	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4944038	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944878	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs500608	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs575096	0.81[EUR][1000 genomes]
rs6592545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7120494	0.87[YRI][hapmap]
rs7121868	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7483884	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826033	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs826039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826048	0.90[YRI][hapmap]
rs826056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826066	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826071	0.87[YRI][hapmap]
rs826072	0.87[YRI][hapmap]
rs826073	0.87[YRI][hapmap]
rs826075	0.86[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10898954	P4HA3	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73730800-73800800	Weak transcription	Fetal Heart	heart
2	chr11:73750800-73800400	Weak transcription	HMEC	breast
3	chr11:73753200-73796400	Weak transcription	Small Intestine	intestine
4	chr11:73753200-73804600	Weak transcription	Colonic Mucosa	Colon
5	chr11:73760000-73802600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:73768800-73798200	Weak transcription	NHEK	skin
7	chr11:73777600-73818600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:73778000-73790600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:73778200-73791000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:73778800-73790400	Strong transcription	Fetal Muscle Leg	muscle
11	chr11:73778800-73790400	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr11:73778800-73792800	Strong transcription	Primary B cells from cord blood	blood
13	chr11:73779000-73792600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:73779200-73791000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr11:73779600-73790800	Strong transcription	Primary T cells from cord blood	blood
16	chr11:73780200-73790400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr11:73780200-73790800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr11:73780600-73790400	Strong transcription	Dnd41	blood
19	chr11:73781200-73795800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:73781800-73849200	Weak transcription	Stomach Mucosa	stomach
21	chr11:73782200-73796400	Weak transcription	Right Ventricle	heart
22	chr11:73782600-73823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr11:73782800-73790400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:73782800-73790600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:73782800-73795400	Weak transcription	K562	blood
26	chr11:73783600-73790400	Strong transcription	Placenta	Placenta
27	chr11:73784200-73796600	Weak transcription	Psoas Muscle	Psoas
28	chr11:73784200-73801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:73785400-73792000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:73785400-73795200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:73785400-73800400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr11:73785600-73795000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:73785600-73796800	Weak transcription	Fetal Kidney	kidney
34	chr11:73785600-73797400	Weak transcription	HUVEC	blood vessel
35	chr11:73785600-73800200	Weak transcription	NH-A	brain
36	chr11:73785600-73803400	Weak transcription	NHDF-Ad	bronchial
37	chr11:73785600-73823600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:73786800-73792400	Strong transcription	HSMMtube	muscle
39	chr11:73786800-73792800	Strong transcription	HSMM	muscle
40	chr11:73787200-73795200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr11:73787400-73790800	Strong transcription	Primary hematopoietic stem cells	blood
42	chr11:73787600-73793000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:73787800-73811400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr11:73788000-73790600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:73788200-73790800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr11:73788200-73792600	Strong transcription	Fetal Brain Female	brain
47	chr11:73788400-73790400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:73788400-73790600	Strong transcription	Liver	Liver
49	chr11:73788400-73790600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:73788400-73790600	Strong transcription	Thymus	Thymus

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