Variant report

Variant	rs11946007
Chromosome Location	chr4:88265937-88265938
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	chr4:88257214..88259344-chr4:88263879..88266042,3	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11097131	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097147	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721653	0.98[EUR][1000 genomes]
rs11726577	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734330	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737402	0.89[EUR][1000 genomes]
rs11930147	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11930151	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11931674	0.81[AFR][1000 genomes]
rs11934060	0.84[AFR][1000 genomes]
rs11939415	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940002	0.80[AFR][1000 genomes]
rs11946391	0.81[AFR][1000 genomes]
rs11946465	0.81[AFR][1000 genomes]
rs12505484	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55663915	0.81[AFR][1000 genomes]
rs55764266	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55878019	0.81[AFR][1000 genomes]
rs55895035	0.91[EUR][1000 genomes]
rs55932175	0.91[EUR][1000 genomes]
rs55974821	0.81[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]
rs56336118	0.81[AFR][1000 genomes]
rs56385009	0.89[EUR][1000 genomes]
rs56390566	0.92[EUR][1000 genomes]
rs56788263	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57088507	0.81[AFR][1000 genomes]
rs57743836	0.81[AFR][1000 genomes]
rs57806008	0.86[AFR][1000 genomes]
rs57948983	0.81[AFR][1000 genomes]
rs58360495	0.91[EUR][1000 genomes]
rs58985971	0.81[AFR][1000 genomes]
rs59037460	0.81[AFR][1000 genomes]
rs59137232	0.81[AFR][1000 genomes]
rs59311794	0.81[AFR][1000 genomes]
rs59476561	0.81[AFR][1000 genomes]
rs59593300	0.81[AFR][1000 genomes]
rs60371489	0.81[AFR][1000 genomes]
rs60597105	0.92[EUR][1000 genomes]
rs60690297	0.81[AFR][1000 genomes]
rs61262236	0.81[AFR][1000 genomes]
rs62305726	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305728	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305729	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62305730	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305731	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305732	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305753	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62319084	0.92[EUR][1000 genomes]
rs72652029	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73839191	0.86[AFR][1000 genomes]
rs73841125	0.84[AFR][1000 genomes]
rs73841126	0.80[AFR][1000 genomes]
rs73841136	0.81[AFR][1000 genomes]
rs73841139	0.81[AFR][1000 genomes]
rs73841140	0.81[AFR][1000 genomes]
rs73841143	0.90[AFR][1000 genomes]
rs7664717	0.88[EUR][1000 genomes]
rs7665549	0.90[EUR][1000 genomes]
rs7665638	0.81[AFR][1000 genomes]
rs7671557	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674658	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690170	0.90[EUR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11946007	HSD17B13	cis	Nerve Tibial	GTEx

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	chr4:88254800-88266000	Weak transcription	Brain Angular Gyrus	brain
3	chr4:88254800-88266000	Weak transcription	Fetal Kidney	kidney
4	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:88255000-88266000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:88255000-88268200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr4:88255000-88292400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:88255200-88267800	Strong transcription	Duodenum Mucosa	Duodenum
9	chr4:88255200-88274400	Weak transcription	GM12878-XiMat	blood
10	chr4:88255200-88285600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:88255200-88293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:88255600-88266200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:88255800-88266200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:88255800-88278200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:88256000-88266000	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:88256000-88266200	Weak transcription	Aorta	Aorta
17	chr4:88256000-88274800	Weak transcription	A549	lung
18	chr4:88256200-88266000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:88256200-88266800	Weak transcription	NHLF	lung
20	chr4:88256200-88267000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:88256200-88267200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:88256200-88292800	Weak transcription	Gastric	stomach
23	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
24	chr4:88256800-88266000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:88257000-88291000	Weak transcription	HUVEC	blood vessel
26	chr4:88257600-88267600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr4:88257800-88311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:88258000-88266800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr4:88258000-88278000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:88258000-88285400	Weak transcription	Small Intestine	intestine
31	chr4:88259200-88277200	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:88259200-88283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:88259400-88267400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr4:88261000-88280000	Weak transcription	Left Ventricle	heart
35	chr4:88261000-88283200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:88261200-88285000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:88261400-88266000	Weak transcription	Brain Germinal Matrix	brain
38	chr4:88262200-88280200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:88262600-88274200	Weak transcription	K562	blood
40	chr4:88262600-88274400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:88262800-88267600	Weak transcription	Ovary	ovary
42	chr4:88263000-88266000	Weak transcription	Adipose Nuclei	Adipose
43	chr4:88263000-88266000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:88263000-88266000	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:88263000-88266000	Weak transcription	Fetal Stomach	stomach
46	chr4:88263000-88266000	Weak transcription	Thymus	Thymus
47	chr4:88263000-88266200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:88263000-88266400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:88263000-88267600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:88263000-88267600	Weak transcription	Placenta	Placenta

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