Variant report

Variant	rs1754435
Chromosome Location	chr9:97366224-97366225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97363139..97364825-chr9:97366128..97368386,2	K562	blood:
2	chr9:97365733..97367940-chr9:97370951..97372481,2	MCF-7	breast:
3	chr9:97363454..97366255-chr9:97375188..97377706,2	K562	blood:
4	chr9:97314619..97316650-chr9:97365797..97368541,2	K562	blood:
5	chr9:97365760..97367307-chr9:97368033..97370545,2	MCF-7	breast:
6	chr9:97343362..97346038-chr9:97364705..97367422,2	MCF-7	breast:
7	chr9:97364234..97367313-chr9:97400419..97403811,3	MCF-7	breast:
8	chr9:97315259..97318533-chr9:97363918..97367292,6	MCF-7	breast:
9	chr9:97315606..97319704-chr9:97363491..97367544,5	MCF-7	breast:
10	chr9:97365715..97366434-chr9:97385051..97385749,2	MCF-7	breast:
11	chr9:97316090..97317268-chr9:97365275..97366675,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000165140	Chromatin interaction
ENSG00000231806	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1042144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821376	0.83[EUR][1000 genomes]
rs10993275	0.87[CEU][hapmap];0.82[CHB][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs10993277	0.83[EUR][1000 genomes]
rs10993278	0.84[EUR][1000 genomes]
rs11999744	0.88[AFR][1000 genomes]
rs12005833	0.88[AFR][1000 genomes]
rs12238876	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13284668	0.86[EUR][1000 genomes]
rs13291835	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13296485	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16937175	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1754439	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];0.83[YRI][hapmap]
rs2296708	0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs2679599	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2679600	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2679602	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs2772022	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2790390	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28369670	0.83[EUR][1000 genomes]
rs28369737	0.88[AFR][1000 genomes]
rs2945802	0.84[TSI][hapmap]
rs2987882	0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs2987897	0.95[CEU][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2993905	0.95[CEU][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2993912	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2993958	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2993959	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2993961	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2993962	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3824484	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3896183	0.83[EUR][1000 genomes]
rs4075984	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4743961	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs4744362	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs479197	0.82[EUR][1000 genomes]
rs514222	0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs515339	0.87[EUR][1000 genomes]
rs540124	0.81[JPT][hapmap];0.84[TSI][hapmap]
rs547834	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs548348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576745	0.87[CEU][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs583365	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs632506	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67721291	0.87[EUR][1000 genomes]
rs693399	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs802918	0.85[EUR][1000 genomes]
rs8192689	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs874248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9695	0.83[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	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
4	nsv466436	chr9:97343620-97369149	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv614917	chr9:97343620-97369149	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1754435	HIATL1	cis	parietal	SCAN
rs1754435	PHF2	cis	cerebellum	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	chr9:97351800-97369200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:97358000-97368800	Weak transcription	Gastric	stomach
4	chr9:97362600-97367000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr9:97364400-97382800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr9:97364800-97382800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr9:97365000-97375400	Genic enhancers	Fetal Intestine Small	intestine
8	chr9:97365000-97376200	Genic enhancers	Liver	Liver
9	chr9:97365200-97367000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:97365200-97369200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:97365400-97366400	Enhancers	Adipose Nuclei	Adipose
12	chr9:97365400-97366400	Enhancers	Fetal Lung	lung
13	chr9:97365400-97366400	Enhancers	Stomach Mucosa	stomach
14	chr9:97365400-97366600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr9:97365400-97366800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:97365400-97366800	Enhancers	Fetal Intestine Large	intestine
17	chr9:97365400-97368800	Enhancers	Colonic Mucosa	Colon
18	chr9:97365600-97366400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:97365600-97366400	Enhancers	Duodenum Mucosa	Duodenum
20	chr9:97365600-97366400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr9:97365600-97366800	Enhancers	Fetal Stomach	stomach
22	chr9:97365600-97367200	Enhancers	Fetal Muscle Leg	muscle
23	chr9:97365800-97366400	Active TSS	Brain Cingulate Gyrus	brain
24	chr9:97365800-97366400	Enhancers	Fetal Thymus	thymus
25	chr9:97365800-97366600	Enhancers	Small Intestine	intestine
26	chr9:97365800-97368200	Weak transcription	Lung	lung
27	chr9:97365800-97370400	Weak transcription	Pancreas	Pancrea
28	chr9:97365800-97373800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:97366000-97366400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:97366000-97366400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr9:97366000-97366400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr9:97366000-97366800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:97366000-97367200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:97366000-97367400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:97366000-97369200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr9:97366000-97369200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr9:97366000-97369600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:97366000-97369600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr9:97366200-97366400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:97366200-97366400	Enhancers	Brain Germinal Matrix	brain
41	chr9:97366200-97366400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr9:97366200-97366600	Enhancers	Brain Hippocampus Middle	brain
43	chr9:97366200-97366800	Enhancers	Primary hematopoietic stem cells	blood
44	chr9:97366200-97366800	Enhancers	Fetal Kidney	kidney
45	chr9:97366200-97367000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr9:97366200-97367400	Enhancers	HepG2	liver
47	chr9:97366200-97369800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:97366200-97369800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr9:97366200-97371600	Weak transcription	Fetal Heart	heart

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