Variant report

Variant	rs10978074
Chromosome Location	chr9:9904481-9904482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10491913	0.90[CHB][hapmap]
rs10978073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10978075	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12238709	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16924754	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034731	chr9:9776126-10481262	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1019399	chr9:9780915-9942126	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1018814	chr9:9793285-9957301	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1019920	chr9:9817031-9925880	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv539984	chr9:9817031-9925880	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1025723	chr9:9817231-9950917	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv539985	chr9:9817231-9950917	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv892295	chr9:9832245-10380406	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1022172	chr9:9841432-9975529	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1015187	chr9:9847852-9944268	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv892296	chr9:9852100-9937753	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1022613	chr9:9857456-9985419	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv539986	chr9:9857456-9985419	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv466147	chr9:9859571-9962204	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv613355	chr9:9859571-9962204	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv613356	chr9:9882950-9926888	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv528854	chr9:9882950-9937753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv973440	chr9:9883691-9929074	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv613357	chr9:9893002-9915186	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv1031495	chr9:9893071-9914486	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1025131	chr9:9893071-9916776	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv1021260	chr9:9893071-9917390	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv892297	chr9:9893071-9937753	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv613358	chr9:9895998-9913373	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv892298	chr9:9895998-9924724	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv471277	chr9:9897866-9912826	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv1020369	chr9:9898577-9938475	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
28	nsv613359	chr9:9904481-10008130	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10978074	LOC400940	trans	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:9884400-9908200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:9901600-9904800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:9902600-9907600	Enhancers	Primary hematopoietic stem cells	blood
4	chr9:9903400-9906200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr9:9903800-9904800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr9:9904000-9905000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr9:9904000-9905200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr9:9904400-9904600	Enhancers	Primary B cells from cord blood	blood
9	chr9:9904400-9907600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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