Variant report

Variant	rs11097131
Chromosome Location	chr4:88266006-88266007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88257214..88259344-chr4:88263879..88266042,3	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11097147	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721653	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs11726577	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734257	1.00[CHB][hapmap]
rs11734330	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737402	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11930147	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11930151	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939415	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939903	0.82[AFR][1000 genomes]
rs11946007	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505484	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923434	1.00[CHB][hapmap]
rs55764266	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55879514	0.82[AFR][1000 genomes]
rs55895035	0.91[EUR][1000 genomes]
rs55932175	0.91[EUR][1000 genomes]
rs56113853	0.80[AFR][1000 genomes]
rs56141705	0.91[EUR][1000 genomes]
rs56258452	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56284919	0.91[EUR][1000 genomes]
rs56385009	0.89[EUR][1000 genomes]
rs56390566	0.92[EUR][1000 genomes]
rs56788263	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58360495	0.91[EUR][1000 genomes]
rs59157345	0.88[AFR][1000 genomes]
rs60597105	0.92[EUR][1000 genomes]
rs60955120	0.82[AFR][1000 genomes]
rs61646372	0.82[AFR][1000 genomes]
rs62305726	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305728	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62305730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305753	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62319084	0.92[EUR][1000 genomes]
rs6531973	1.00[CHD][hapmap];0.82[MEX][hapmap]
rs6531985	1.00[CHD][hapmap]
rs6811010	1.00[CHD][hapmap]
rs6849846	1.00[CHD][hapmap]
rs72652029	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73839192	0.88[AFR][1000 genomes]
rs73841141	0.89[AFR][1000 genomes]
rs73841142	0.89[AFR][1000 genomes]
rs73841144	0.89[AFR][1000 genomes]
rs73841145	0.89[AFR][1000 genomes]
rs7664717	0.88[EUR][1000 genomes]
rs7665549	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs7665638	0.87[YRI][hapmap]
rs7667669	1.00[CHB][hapmap]
rs7668684	1.00[CHB][hapmap]
rs7671557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682516	1.00[CHD][hapmap]
rs7682892	1.00[CHD][hapmap]
rs7690170	0.90[EUR][1000 genomes]
rs9684766	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv4412	chr4:88237813-88283368	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11097131	JAM3	trans	lymphoblastoid	seeQTL
rs11097131	HSD17B13	cis	cerebellum	SCAN
rs11097131	CASK	trans	lymphoblastoid	seeQTL
rs11097131	HSD17B13	cis	Nerve Tibial	GTEx
rs11097131	HSD17B13	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88253800-88274600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:88255000-88268200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:88255000-88292400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:88255200-88267800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr4:88255200-88274400	Weak transcription	GM12878-XiMat	blood
7	chr4:88255200-88285600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:88255200-88293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:88255600-88266200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:88255800-88266200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:88255800-88278200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:88256000-88266200	Weak transcription	Aorta	Aorta
13	chr4:88256000-88274800	Weak transcription	A549	lung
14	chr4:88256200-88266800	Weak transcription	NHLF	lung
15	chr4:88256200-88267000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:88256200-88267200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:88256200-88292800	Weak transcription	Gastric	stomach
18	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
19	chr4:88257000-88291000	Weak transcription	HUVEC	blood vessel
20	chr4:88257600-88267600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr4:88257800-88311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:88258000-88266800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr4:88258000-88278000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:88258000-88285400	Weak transcription	Small Intestine	intestine
25	chr4:88259200-88277200	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:88259200-88283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:88259400-88267400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr4:88261000-88280000	Weak transcription	Left Ventricle	heart
29	chr4:88261000-88283200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:88261200-88285000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:88262200-88280200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:88262600-88274200	Weak transcription	K562	blood
33	chr4:88262600-88274400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:88262800-88267600	Weak transcription	Ovary	ovary
35	chr4:88263000-88266200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:88263000-88266400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:88263000-88267600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:88263000-88267600	Weak transcription	Placenta	Placenta
39	chr4:88263000-88274600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:88263000-88274600	Weak transcription	Colonic Mucosa	Colon
41	chr4:88263000-88277000	Weak transcription	Lung	lung
42	chr4:88263000-88277000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:88263000-88278000	Weak transcription	Stomach Mucosa	stomach
44	chr4:88263000-88280000	Weak transcription	Pancreas	Pancrea
45	chr4:88263200-88281600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr4:88263400-88266200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:88263400-88267400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:88263600-88266800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:88263600-88274600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr4:88264000-88277000	Weak transcription	HSMM	muscle

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