Variant report

Variant	rs4869256
Chromosome Location	chr5:95401970-95401971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95398261..95399913-chr5:95401508..95403607,2	K562	blood:
2	chr5:95194068..95196070-chr5:95401310..95403656,2	K562	blood:
3	chr5:95401885..95403759-chr5:95409386..95411340,2	K562	blood:
4	chr5:95401831..95405579-chr5:95411274..95417557,7	K562	blood:

Variant related genes	Relation type
ENSG00000207578	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10056771	0.81[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs10079268	0.87[EUR][1000 genomes]
rs10085034	0.81[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11740207	0.82[EUR][1000 genomes]
rs11949461	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11951463	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11956456	0.82[EUR][1000 genomes]
rs11960219	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13155375	0.81[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs13172783	0.81[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs13186419	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1389827	0.87[EUR][1000 genomes]
rs1870270	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2067498	0.80[EUR][1000 genomes]
rs4128178	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4270717	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4416625	1.00[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4479864	0.95[EUR][1000 genomes]
rs4513721	0.82[EUR][1000 genomes]
rs4869258	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4869259	0.82[EUR][1000 genomes]
rs4869260	0.82[EUR][1000 genomes]
rs4869266	0.80[EUR][1000 genomes]
rs4998057	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6556899	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6556900	0.85[EUR][1000 genomes]
rs66683317	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6866723	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6873504	0.82[EUR][1000 genomes]
rs6879658	0.95[EUR][1000 genomes]
rs6879847	0.95[EUR][1000 genomes]
rs6884999	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6889697	0.82[EUR][1000 genomes]
rs6894768	0.82[EUR][1000 genomes]
rs6895121	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6895146	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7341111	0.82[EUR][1000 genomes]
rs7700425	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7702346	0.80[EUR][1000 genomes]
rs7702646	0.80[EUR][1000 genomes]
rs7710337	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7717351	0.84[EUR][1000 genomes]
rs7734224	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7734985	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs9314163	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9314164	0.92[EUR][1000 genomes]
rs9314165	0.82[EUR][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	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv823146	chr5:95300912-95453557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	esv2757121	chr5:95304236-95539536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	esv34203	chr5:95310985-95452324	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv522097	chr5:95347786-95425199	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv522465	chr5:95347786-95425199	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4869256	SPATA9	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95399000-95403800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:95399600-95403600	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr5:95400200-95402000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr5:95400400-95402000	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr5:95400400-95402200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:95400400-95402200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:95400400-95402600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr5:95400400-95402800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:95400400-95403200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:95400600-95402000	Enhancers	HSMMtube	muscle
11	chr5:95400600-95402200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:95400600-95402200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:95400600-95403000	Enhancers	A549	lung
14	chr5:95400600-95403200	Enhancers	HSMM	muscle
15	chr5:95400600-95403400	Enhancers	Hela-S3	cervix
16	chr5:95400600-95403600	Enhancers	HUVEC	blood vessel
17	chr5:95400600-95403600	Enhancers	NHDF-Ad	bronchial
18	chr5:95400600-95403600	Enhancers	NHEK	skin
19	chr5:95400600-95404200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:95400600-95404400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:95400600-95404800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:95400600-95404800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:95400600-95404800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:95400600-95404800	Enhancers	HMEC	breast
25	chr5:95400800-95402000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr5:95401200-95402000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr5:95401200-95402200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr5:95401200-95402200	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr5:95401200-95402200	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr5:95401200-95402200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr5:95401200-95404400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:95401200-95404400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:95401200-95404800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr5:95401400-95402200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:95401400-95402200	Enhancers	Colonic Mucosa	Colon
36	chr5:95401400-95402200	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr5:95401400-95402200	Enhancers	HepG2	liver
38	chr5:95401400-95402800	Enhancers	Fetal Intestine Large	intestine
39	chr5:95401400-95402800	Enhancers	Fetal Intestine Small	intestine
40	chr5:95401400-95403200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:95401400-95403400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:95401400-95403400	Enhancers	NH-A	brain
43	chr5:95401400-95403400	Enhancers	Osteobl	bone
44	chr5:95401400-95403600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:95401400-95404200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:95401400-95405000	Enhancers	NHLF	lung
47	chr5:95401600-95402000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:95401600-95402000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr5:95401600-95402000	Enhancers	Fetal Kidney	kidney
50	chr5:95401600-95402000	Enhancers	Stomach Mucosa	stomach

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