Variant report

Variant	rs7025878
Chromosome Location	chr9:97198792-97198793
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10114295	0.83[EUR][1000 genomes]
rs10115864	0.88[ASN][1000 genomes]
rs10116979	0.83[EUR][1000 genomes]
rs10122398	0.88[ASN][1000 genomes]
rs10125631	0.83[EUR][1000 genomes]
rs10125744	0.88[ASN][1000 genomes]
rs10283669	0.83[ASN][1000 genomes]
rs10441776	0.83[EUR][1000 genomes]
rs1061835	0.83[ASN][1000 genomes]
rs10993191	0.85[ASN][1000 genomes]
rs10993194	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10993201	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11793128	0.82[JPT][hapmap]
rs11795331	0.82[JPT][hapmap]
rs12338230	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12338572	0.88[ASN][1000 genomes]
rs12341403	0.83[ASN][1000 genomes]
rs12343123	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12343977	0.83[EUR][1000 genomes]
rs1536690	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs16911832	0.83[EUR][1000 genomes]
rs1878875	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2406663	0.83[EUR][1000 genomes]
rs28459299	0.83[EUR][1000 genomes]
rs28477240	0.83[EUR][1000 genomes]
rs28575335	0.83[EUR][1000 genomes]
rs28715696	0.83[EUR][1000 genomes]
rs28802403	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4744330	0.85[JPT][hapmap]
rs55936246	0.88[ASN][1000 genomes]
rs55962682	0.88[ASN][1000 genomes]
rs56413623	0.83[EUR][1000 genomes]
rs6479541	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6479545	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6479549	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7019137	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7022386	0.83[EUR][1000 genomes]
rs7027704	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7027860	0.83[EUR][1000 genomes]
rs7028388	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7030326	0.83[ASN][1000 genomes]
rs7030967	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7034153	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7036474	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7037298	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7041219	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7042219	0.83[EUR][1000 genomes]
rs7042434	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7042468	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7045712	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7046779	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs722353	1.00[JPT][hapmap]
rs73529936	0.85[EUR][1000 genomes]
rs7850084	0.81[EUR][1000 genomes]
rs7856786	0.83[ASN][1000 genomes]
rs7858126	0.82[EUR][1000 genomes]
rs7859571	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs7859955	0.83[ASN][1000 genomes]
rs7868600	0.83[EUR][1000 genomes]
rs7868703	0.83[EUR][1000 genomes]
rs7873527	0.84[EUR][1000 genomes]
rs7874441	0.85[JPT][hapmap]
rs9299417	0.82[JPT][hapmap]
rs9632920	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv982324	chr9:97139062-97200156	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
6	esv33917	chr9:97185592-97216212	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv893593	chr9:97196979-97228918	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7025878	HIATL1	Cis_1M	lymphoblastoid	RTeQTL
rs7025878	FLJ14753	cis	multi-tissue	Pritchard
rs7025878	HIATL1	cis	multi-tissue	Pritchard
rs7025878	HIATL1	cis	Lymphoblastoid	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97158000-97203200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr9:97160400-97203600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr9:97166400-97206400	Weak transcription	HSMMtube	muscle
4	chr9:97167800-97203600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:97169800-97207000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:97172000-97203200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr9:97172000-97208400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr9:97172600-97204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:97174200-97207000	Weak transcription	Lung	lung
10	chr9:97175600-97204200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr9:97175800-97202200	Weak transcription	Dnd41	blood
12	chr9:97176000-97203800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:97176200-97201000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr9:97176200-97203200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:97176200-97203600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:97176200-97203600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:97176200-97207000	Weak transcription	Left Ventricle	heart
18	chr9:97176400-97203200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr9:97176600-97203400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr9:97176800-97203200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:97176800-97203600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:97176800-97218000	Weak transcription	Fetal Brain Female	brain
23	chr9:97177000-97203200	Weak transcription	Osteobl	bone
24	chr9:97177200-97201000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:97177200-97201000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:97177200-97203600	Weak transcription	Thymus	Thymus
27	chr9:97177200-97209400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:97177400-97201400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr9:97177400-97201400	Weak transcription	Fetal Thymus	thymus
30	chr9:97177400-97206400	Weak transcription	Gastric	stomach
31	chr9:97178000-97203800	Weak transcription	K562	blood
32	chr9:97178200-97201000	Weak transcription	Fetal Muscle Leg	muscle
33	chr9:97178400-97203600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:97178400-97206800	Weak transcription	Esophagus	oesophagus
35	chr9:97179600-97201000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:97179800-97203200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:97180200-97201600	Weak transcription	Primary B cells from cord blood	blood
38	chr9:97180200-97203600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:97180400-97201000	Weak transcription	HSMM	muscle
40	chr9:97180400-97203600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr9:97180600-97201600	Weak transcription	Hela-S3	cervix
42	chr9:97180800-97203200	Weak transcription	GM12878-XiMat	blood
43	chr9:97181000-97204800	Weak transcription	Placenta	Placenta
44	chr9:97181000-97208400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr9:97181400-97215800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:97181600-97206400	Weak transcription	HUVEC	blood vessel
47	chr9:97182400-97203600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:97182600-97201000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:97182600-97203000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr9:97182800-97200800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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