Variant report

Variant	rs12236578
Chromosome Location	chr9:97201550-97201551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97200618..97202652-chr9:97218281..97220232,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10821345	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10821352	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10993182	0.81[ASN][1000 genomes]
rs10993193	0.80[EUR][1000 genomes]
rs10993210	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11789704	0.90[ASN][1000 genomes]
rs12002028	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12004014	0.90[EUR][1000 genomes]
rs16909983	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16910109	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1752784	0.81[ASN][1000 genomes]
rs2104642	0.81[EUR][1000 genomes]
rs2486620	0.80[ASN][1000 genomes]
rs2486632	0.94[ASN][1000 genomes]
rs2769813	0.80[ASN][1000 genomes]
rs2993948	0.81[ASN][1000 genomes]
rs4612412	0.94[ASN][1000 genomes]
rs4744345	0.94[ASN][1000 genomes]
rs55877910	0.81[ASN][1000 genomes]
rs56074891	0.81[EUR][1000 genomes]
rs56987829	0.88[EUR][1000 genomes]
rs60964095	0.81[ASN][1000 genomes]
rs61628907	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs639276	0.96[ASN][1000 genomes]
rs9409544	0.83[ASN][1000 genomes]
rs9409546	0.94[ASN][1000 genomes]
rs9409550	0.90[ASN][1000 genomes]
rs9409564	0.91[ASN][1000 genomes]
rs9409565	0.84[ASN][1000 genomes]
rs9409567	0.85[ASN][1000 genomes]
rs9409767	0.91[ASN][1000 genomes]
rs9409771	0.89[ASN][1000 genomes]
rs9409778	0.91[ASN][1000 genomes]
rs9409780	0.86[ASN][1000 genomes]
rs9409787	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv33917	chr9:97185592-97216212	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12236578	HIATL1	cis	Whole Blood	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

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	chr9:97176200-97203200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr9:97176200-97203600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:97176200-97203600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:97176200-97207000	Weak transcription	Left Ventricle	heart
17	chr9:97176400-97203200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:97176600-97203400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr9:97176800-97203200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:97176800-97203600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr9:97176800-97218000	Weak transcription	Fetal Brain Female	brain
22	chr9:97177000-97203200	Weak transcription	Osteobl	bone
23	chr9:97177200-97203600	Weak transcription	Thymus	Thymus
24	chr9:97177200-97209400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:97177400-97206400	Weak transcription	Gastric	stomach
26	chr9:97178000-97203800	Weak transcription	K562	blood
27	chr9:97178400-97203600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:97178400-97206800	Weak transcription	Esophagus	oesophagus
29	chr9:97179800-97203200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:97180200-97201600	Weak transcription	Primary B cells from cord blood	blood
31	chr9:97180200-97203600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:97180400-97203600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:97180600-97201600	Weak transcription	Hela-S3	cervix
34	chr9:97180800-97203200	Weak transcription	GM12878-XiMat	blood
35	chr9:97181000-97204800	Weak transcription	Placenta	Placenta
36	chr9:97181000-97208400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr9:97181400-97215800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:97181600-97206400	Weak transcription	HUVEC	blood vessel
39	chr9:97182400-97203600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:97182600-97203000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr9:97182800-97202000	Weak transcription	A549	lung
42	chr9:97183000-97212000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:97183800-97203200	Weak transcription	Adipose Nuclei	Adipose
44	chr9:97184400-97203200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:97184400-97203600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:97185000-97203600	Weak transcription	Primary T cells from cord blood	blood
47	chr9:97186200-97204200	Weak transcription	Spleen	Spleen
48	chr9:97187600-97205200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr9:97190000-97202800	Weak transcription	Liver	Liver
50	chr9:97190400-97215800	Weak transcription	Ovary	ovary

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