Variant report

Variant	rs1478938
Chromosome Location	chr9:5931216-5931217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:5924252..5926200-chr9:5929178..5931447,2	MCF-7	breast:
2	chr9:5913974..5916739-chr9:5930124..5932087,2	K562	blood:
3	chr9:5930058..5932668-chr9:5946497..5948957,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10121480	0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs10733520	0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs10733521	0.81[ASN][1000 genomes]
rs10733522	0.81[ASN][1000 genomes]
rs10739079	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10739082	0.82[ASN][1000 genomes]
rs10758731	0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10758732	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs10758734	0.81[JPT][hapmap]
rs10815330	0.89[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs10815335	0.84[CHD][hapmap];0.87[JPT][hapmap]
rs1331378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1331379	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1411948	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs1478937	0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17494996	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs186913	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1888703	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1888704	0.82[ASN][1000 genomes]
rs2045959	0.81[EUR][1000 genomes]
rs2150703	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2169906	0.82[ASN][1000 genomes]
rs2244053	1.00[JPT][hapmap]
rs2244058	1.00[JPT][hapmap]
rs2291055	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs2381341	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2381360	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2890690	0.81[ASN][1000 genomes]
rs343500	0.84[GIH][hapmap]
rs3739649	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs3933800	0.84[ASN][1000 genomes]
rs4389996	0.87[JPT][hapmap]
rs4395943	0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap]
rs4740833	0.89[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs4740834	0.82[ASN][1000 genomes]
rs4742131	1.00[JPT][hapmap]
rs4742142	0.81[ASN][1000 genomes]
rs4742143	0.81[ASN][1000 genomes]
rs58909954	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6477017	1.00[JPT][hapmap]
rs6477022	0.81[ASN][1000 genomes]
rs6477023	0.82[ASN][1000 genomes]
rs6477024	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7021498	0.81[ASN][1000 genomes]
rs7024130	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7026453	0.81[ASN][1000 genomes]
rs7026454	0.81[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7029054	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7029833	0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7032130	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs7044750	0.82[ASN][1000 genomes]
rs7856075	0.89[ASN][1000 genomes]
rs7859471	0.88[CEU][hapmap]
rs7868062	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv613204	chr9:5931216-5971977	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5898400-5947200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:5919000-5939800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:5919800-5935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:5920800-5938800	Weak transcription	Small Intestine	intestine
5	chr9:5921200-5939800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:5921200-5950400	Weak transcription	Psoas Muscle	Psoas
7	chr9:5922000-5941600	Weak transcription	HSMMtube	muscle
8	chr9:5922200-5935800	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:5922400-5933400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr9:5922400-5935000	Weak transcription	Pancreas	Pancrea
11	chr9:5922400-5935200	Weak transcription	HMEC	breast
12	chr9:5922400-5939800	Weak transcription	Gastric	stomach
13	chr9:5922600-5947000	Weak transcription	Fetal Heart	heart
14	chr9:5923000-5936200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr9:5923000-5945200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:5923000-5969000	Weak transcription	Fetal Stomach	stomach
17	chr9:5923200-5933400	Weak transcription	Left Ventricle	heart
18	chr9:5923200-5933600	Weak transcription	Fetal Lung	lung
19	chr9:5923200-5934000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:5923200-5934200	Weak transcription	Colonic Mucosa	Colon
21	chr9:5923200-5934800	Weak transcription	Dnd41	blood
22	chr9:5923200-5935000	Weak transcription	Spleen	Spleen
23	chr9:5923200-5935000	Weak transcription	HepG2	liver
24	chr9:5923200-5935200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:5923200-5935800	Weak transcription	HUVEC	blood vessel
26	chr9:5923200-5938800	Weak transcription	Right Ventricle	heart
27	chr9:5923200-5939000	Weak transcription	Lung	lung
28	chr9:5923200-5939600	Weak transcription	Brain Angular Gyrus	brain
29	chr9:5923200-5943000	Weak transcription	Esophagus	oesophagus
30	chr9:5923200-5947600	Weak transcription	Fetal Kidney	kidney
31	chr9:5923200-5949200	Weak transcription	NHLF	lung
32	chr9:5923200-5968200	Weak transcription	Fetal Muscle Leg	muscle
33	chr9:5923200-5971800	Weak transcription	NHEK	skin
34	chr9:5923200-5972400	Weak transcription	Aorta	Aorta
35	chr9:5923400-5931600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr9:5923400-5933400	Weak transcription	Thymus	Thymus
37	chr9:5923400-5935800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:5923400-5939400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr9:5923400-5939600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr9:5924400-5935200	Weak transcription	Fetal Thymus	thymus
41	chr9:5924400-5935600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr9:5924600-5931800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr9:5924600-5935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:5924600-5939600	Weak transcription	Brain Hippocampus Middle	brain
45	chr9:5924600-5942600	Weak transcription	Brain Germinal Matrix	brain
46	chr9:5924600-5945200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr9:5924600-5946800	Weak transcription	Brain Substantia Nigra	brain
48	chr9:5924600-5949200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr9:5924600-5967400	Weak transcription	Brain Anterior Caudate	brain
50	chr9:5924600-5968600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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