Variant report

Variant	rs4477096
Chromosome Location	chr9:97208699-97208700
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97206178..97208805-chr9:97213845..97216691,2	K562	blood:
2	chr9:97204620..97207468-chr9:97208573..97210873,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs12342163	0.82[YRI][hapmap]
rs1310977	0.89[CEU][hapmap];0.81[ASN][1000 genomes]
rs16912862	0.91[CHB][hapmap]
rs1752786	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2006685	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2049008	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2265535	0.80[ASN][1000 genomes]
rs2277182	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479602	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2769119	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2986859	0.85[ASN][1000 genomes]
rs2987115	0.85[ASN][1000 genomes]
rs3131910	0.86[CHB][hapmap]
rs4434674	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4497033	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4509403	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743953	0.81[ASN][1000 genomes]
rs4743954	0.85[ASN][1000 genomes]
rs4743955	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744336	0.85[CEU][hapmap]
rs4744346	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs600442	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479537	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6479544	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs670230	0.96[CEU][hapmap];0.90[YRI][hapmap]
rs684892	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688165	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7020879	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7023744	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7023915	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7024159	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025755	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027465	0.86[ASN][1000 genomes]
rs7027489	0.82[ASN][1000 genomes]
rs7029113	0.93[CEU][hapmap]
rs7031088	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7031496	0.87[ASN][1000 genomes]
rs7031949	0.82[ASN][1000 genomes]
rs7037190	0.82[ASN][1000 genomes]
rs7037198	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7040577	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040710	0.85[ASN][1000 genomes]
rs7047279	0.88[ASN][1000 genomes]
rs7047295	0.86[ASN][1000 genomes]
rs7047930	0.85[ASN][1000 genomes]
rs7048688	0.82[ASN][1000 genomes]
rs7848221	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7848227	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7853182	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7860616	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7863310	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7863312	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7868562	0.84[ASN][1000 genomes]
rs9299421	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9299422	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9409511	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9409512	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9409513	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9409552	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409759	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9409763	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409765	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409777	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9409779	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9696557	0.92[CEU][hapmap]
rs9696843	0.82[CHB][hapmap]
rs9777207	0.96[EUR][1000 genomes];0.89[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4477096	RP11-307E17.8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97176800-97218000	Weak transcription	Fetal Brain Female	brain
2	chr9:97177200-97209400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:97181400-97215800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:97183000-97212000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:97190400-97215800	Weak transcription	Ovary	ovary
6	chr9:97192200-97210000	Weak transcription	NHDF-Ad	bronchial
7	chr9:97192200-97221600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:97193000-97211600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr9:97193800-97216000	Weak transcription	Brain Substantia Nigra	brain
10	chr9:97194000-97216000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:97194400-97211800	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:97195200-97211800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:97195200-97216000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:97195200-97216000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:97195600-97213000	Weak transcription	Fetal Intestine Small	intestine
16	chr9:97195600-97218000	Weak transcription	Pancreas	Pancrea
17	chr9:97199400-97221400	Weak transcription	Psoas Muscle	Psoas
18	chr9:97199600-97209800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr9:97199600-97211600	Weak transcription	Fetal Kidney	kidney
20	chr9:97200000-97211000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:97201000-97223400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:97201000-97224600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr9:97201000-97225000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr9:97201000-97225800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:97201400-97221400	Weak transcription	Stomach Mucosa	stomach
26	chr9:97201400-97225200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:97201600-97209000	Weak transcription	Fetal Lung	lung
28	chr9:97201600-97224800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:97202000-97211200	Weak transcription	NH-A	brain
30	chr9:97202000-97211800	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:97202000-97224200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr9:97202200-97215800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:97202200-97216000	Weak transcription	Brain Angular Gyrus	brain
34	chr9:97202200-97225600	Strong transcription	Dnd41	blood
35	chr9:97202400-97222600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr9:97202800-97209800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:97202800-97211800	Weak transcription	Brain Germinal Matrix	brain
38	chr9:97203000-97215800	Weak transcription	Brain Anterior Caudate	brain
39	chr9:97203200-97214000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr9:97203200-97225000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:97203400-97211800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:97203600-97212400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr9:97203600-97212400	Strong transcription	Primary T cells from cord blood	blood
44	chr9:97203600-97212400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr9:97203600-97214000	Strong transcription	Primary B cells from cord blood	blood
46	chr9:97203800-97217000	Weak transcription	HepG2	liver
47	chr9:97204000-97211400	Weak transcription	Colonic Mucosa	Colon
48	chr9:97204000-97215800	Weak transcription	Small Intestine	intestine
49	chr9:97204000-97215800	Weak transcription	NHLF	lung
50	chr9:97204200-97222800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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