Variant report

Variant	rs1754439
Chromosome Location	chr9:97370624-97370625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97369469..97371530-chr9:97378423..97380826,2	K562	blood:
2	chr9:97368983..97370788-chr9:97391157..97393414,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1042144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821376	0.85[EUR][1000 genomes]
rs10993275	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10993277	0.85[EUR][1000 genomes]
rs10993278	0.84[EUR][1000 genomes]
rs12238876	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13284668	0.88[EUR][1000 genomes]
rs13291835	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13296485	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16937175	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs1754435	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1999122	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2017136	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2296708	0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs2679599	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2679600	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2679602	0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs2772022	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2790390	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28369670	0.85[EUR][1000 genomes]
rs2945802	1.00[ASW][hapmap];0.86[TSI][hapmap]
rs2987882	0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2987897	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993905	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2993912	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2993958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2993959	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2993961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2993962	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3824484	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3896183	0.85[EUR][1000 genomes]
rs4075984	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4743961	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs4744362	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs479197	0.84[EUR][1000 genomes]
rs514222	0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs515339	0.89[EUR][1000 genomes]
rs540124	1.00[ASW][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs547834	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs548348	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576745	0.83[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs583365	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs632506	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67721291	0.89[EUR][1000 genomes]
rs693399	0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs802918	0.87[EUR][1000 genomes]
rs8192689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs874248	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9695	0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1754439	PHF2	cis	cerebellum	SCAN
rs1754439	HIATL1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97347600-97374000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:97364400-97382800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr9:97364800-97382800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr9:97365000-97375400	Genic enhancers	Fetal Intestine Small	intestine
5	chr9:97365000-97376200	Genic enhancers	Liver	Liver
6	chr9:97365800-97373800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:97366200-97371600	Weak transcription	Fetal Heart	heart
8	chr9:97366600-97384400	Weak transcription	Small Intestine	intestine
9	chr9:97367000-97370800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:97368400-97375200	Enhancers	Stomach Mucosa	stomach
11	chr9:97368800-97370800	Flanking Active TSS	HepG2	liver
12	chr9:97369200-97370800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr9:97369200-97370800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr9:97369200-97371200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr9:97369200-97371800	Enhancers	Fetal Intestine Large	intestine
16	chr9:97369200-97372400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:97369400-97371200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:97369400-97372000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:97369400-97372200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:97369400-97373400	Enhancers	Fetal Lung	lung
21	chr9:97369600-97371200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr9:97369600-97371200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr9:97369800-97370800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr9:97369800-97371200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr9:97369800-97371800	Weak transcription	Gastric	stomach
26	chr9:97369800-97372600	Enhancers	Placenta	Placenta
27	chr9:97370000-97370800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr9:97370000-97370800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:97370000-97370800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
30	chr9:97370000-97370800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:97370000-97372200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:97370000-97382400	Weak transcription	Lung	lung
33	chr9:97370200-97370800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:97370200-97370800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:97370400-97370800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr9:97370400-97370800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr9:97370400-97370800	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr9:97370400-97370800	Enhancers	Fetal Muscle Leg	muscle
39	chr9:97370400-97371600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr9:97370400-97372400	Enhancers	Pancreas	Pancrea
41	chr9:97370600-97370800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:97370600-97370800	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr9:97370600-97370800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:97370600-97370800	Enhancers	Brain Germinal Matrix	brain
45	chr9:97370600-97370800	Bivalent Enhancer	Fetal Thymus	thymus
46	chr9:97370600-97371400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr9:97370600-97371800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr9:97370600-97371800	Enhancers	Fetal Stomach	stomach
49	chr9:97370600-97375200	Weak transcription	Colonic Mucosa	Colon

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