Variant report

Variant	rs688165
Chromosome Location	chr9:97204130-97204131
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	chr9:97202408..97204318-chr9:97206434..97208098,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10821325	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[MKK][hapmap]
rs10821326	0.83[CHB][hapmap];1.00[MKK][hapmap]
rs16912862	0.85[CHB][hapmap]
rs1752786	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1752787	0.82[AMR][1000 genomes]
rs2049008	0.83[ASN][1000 genomes]
rs2277182	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2479601	1.00[CEU][hapmap]
rs2479602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2769119	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2945802	0.90[MKK][hapmap]
rs3118756	0.84[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs3131899	0.86[CHD][hapmap];1.00[MKK][hapmap]
rs3131910	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap]
rs4477096	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4509403	0.85[ASN][1000 genomes]
rs4743953	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4743954	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743955	0.85[ASN][1000 genomes]
rs4744340	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744346	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs540124	1.00[MKK][hapmap]
rs6479537	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs684892	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7020879	0.83[ASN][1000 genomes]
rs7024159	0.85[ASN][1000 genomes]
rs7025755	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7027465	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7027489	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7031088	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7031496	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7031949	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7037190	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7037198	0.83[ASN][1000 genomes]
rs7040710	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7047279	0.83[ASN][1000 genomes]
rs7047295	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7047930	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7048688	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7848227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7853182	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7860616	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7868562	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7873525	0.82[ASN][1000 genomes]
rs9299421	0.85[ASN][1000 genomes]
rs9299422	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9409511	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9409512	0.86[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap]
rs9409513	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9409759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9409765	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs9409777	0.83[ASN][1000 genomes]
rs9409779	0.83[ASN][1000 genomes]
rs9409792	0.81[EUR][1000 genomes]
rs9696843	0.81[CHD][hapmap]
rs9777207	0.84[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	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs688165	RP11-307E17.8	cis	Esophagus Muscularis	GTEx
rs688165	HIATL1	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97166400-97206400	Weak transcription	HSMMtube	muscle
2	chr9:97169800-97207000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:97172000-97208400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:97172600-97204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:97174200-97207000	Weak transcription	Lung	lung
6	chr9:97175600-97204200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:97176200-97207000	Weak transcription	Left Ventricle	heart
8	chr9:97176800-97218000	Weak transcription	Fetal Brain Female	brain
9	chr9:97177200-97209400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:97177400-97206400	Weak transcription	Gastric	stomach
11	chr9:97178400-97206800	Weak transcription	Esophagus	oesophagus
12	chr9:97181000-97204800	Weak transcription	Placenta	Placenta
13	chr9:97181000-97208400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr9:97181400-97215800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:97181600-97206400	Weak transcription	HUVEC	blood vessel
16	chr9:97183000-97212000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:97186200-97204200	Weak transcription	Spleen	Spleen
18	chr9:97187600-97205200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:97190400-97215800	Weak transcription	Ovary	ovary
20	chr9:97191600-97208200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:97192200-97210000	Weak transcription	NHDF-Ad	bronchial
22	chr9:97192200-97221600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:97193000-97211600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr9:97193800-97216000	Weak transcription	Brain Substantia Nigra	brain
25	chr9:97194000-97206600	Weak transcription	Right Ventricle	heart
26	chr9:97194000-97216000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr9:97194200-97208200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:97194400-97211800	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:97195200-97211800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:97195200-97216000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:97195200-97216000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:97195600-97213000	Weak transcription	Fetal Intestine Small	intestine
33	chr9:97195600-97218000	Weak transcription	Pancreas	Pancrea
34	chr9:97199400-97221400	Weak transcription	Psoas Muscle	Psoas
35	chr9:97199600-97209800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:97199600-97211600	Weak transcription	Fetal Kidney	kidney
37	chr9:97200000-97204200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr9:97200000-97211000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:97200800-97204600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:97201000-97205600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:97201000-97206200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:97201000-97223400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:97201000-97224600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr9:97201000-97225000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr9:97201000-97225800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr9:97201200-97206200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:97201400-97221400	Weak transcription	Stomach Mucosa	stomach
48	chr9:97201400-97225200	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr9:97201600-97209000	Weak transcription	Fetal Lung	lung
50	chr9:97201600-97224800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links