Variant report

Variant	rs11734330
Chromosome Location	chr4:88274740-88274741
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:88274380..88275024-chr4:88386955..88387766,2	MCF-7	breast:
2	chr4:88274412..88275303-chr4:88464991..88465582,2	MCF-7	breast:
3	chr4:88274390..88275203-chr4:88387077..88388072,3	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs11097131	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]
rs11097147	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721653	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11726577	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734257	1.00[CHB][hapmap]
rs11737402	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11930147	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11930151	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940002	0.80[AFR][1000 genomes]
rs11946007	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946391	0.81[AFR][1000 genomes]
rs11946465	0.81[AFR][1000 genomes]
rs12505484	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923434	1.00[CHB][hapmap]
rs55663915	0.81[AFR][1000 genomes]
rs55764266	0.88[EUR][1000 genomes]
rs55878019	0.81[AFR][1000 genomes]
rs55895035	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55932175	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55974821	0.81[AFR][1000 genomes]
rs56141705	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56258452	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56284919	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56336118	0.81[AFR][1000 genomes]
rs56385009	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56390566	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56788263	0.89[AFR][1000 genomes];0.97[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	0.90[AMR][1000 genomes];0.93[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	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60690297	0.81[AFR][1000 genomes]
rs61262236	0.81[AFR][1000 genomes]
rs62305726	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305728	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305729	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs62305730	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305731	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305732	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305753	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62319084	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6531973	1.00[CHD][hapmap]
rs6531985	1.00[CHD][hapmap]
rs6811010	1.00[CHD][hapmap]
rs6820688	0.80[YRI][hapmap]
rs6849846	1.00[CHD][hapmap]
rs72652029	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[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	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7665549	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7665638	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs7667669	1.00[CHB][hapmap]
rs7668684	1.00[CHB][hapmap]
rs7671557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682516	1.00[CHD][hapmap]
rs7682892	1.00[CHD][hapmap]
rs7690170	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7698406	0.82[YRI][hapmap]
rs9684766	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	esv2559237	chr4:88267456-88274841	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3388226	chr4:88267578-88275176	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11734330	HSD17B13	cis	cerebellum	SCAN
rs11734330	HSD17B13	cis	Nerve Tibial	GTEx
rs11734330	HSD17B13	cis	parietal	SCAN
rs11734330	JAM3	trans	lymphoblastoid	seeQTL
rs11734330	CASK	trans	lymphoblastoid	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:88255000-88292400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:88255200-88285600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:88255200-88293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:88255800-88278200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:88256000-88274800	Weak transcription	A549	lung
7	chr4:88256200-88292800	Weak transcription	Gastric	stomach
8	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
9	chr4:88257000-88291000	Weak transcription	HUVEC	blood vessel
10	chr4:88257800-88311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:88258000-88278000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:88258000-88285400	Weak transcription	Small Intestine	intestine
13	chr4:88259200-88277200	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:88259200-88283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:88261000-88280000	Weak transcription	Left Ventricle	heart
16	chr4:88261000-88283200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:88261200-88285000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:88262200-88280200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:88263000-88277000	Weak transcription	Lung	lung
20	chr4:88263000-88277000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:88263000-88278000	Weak transcription	Stomach Mucosa	stomach
22	chr4:88263000-88280000	Weak transcription	Pancreas	Pancrea
23	chr4:88263200-88281600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:88264000-88277000	Weak transcription	HSMM	muscle
25	chr4:88264200-88285600	Weak transcription	Spleen	Spleen
26	chr4:88264400-88279800	Weak transcription	Hela-S3	cervix
27	chr4:88266200-88285000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:88266400-88275000	Weak transcription	Aorta	Aorta
29	chr4:88266400-88278200	Weak transcription	Brain Angular Gyrus	brain
30	chr4:88266400-88292200	Weak transcription	Fetal Brain Male	brain
31	chr4:88266600-88275000	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:88266600-88275200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:88266600-88275200	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:88266600-88278000	Weak transcription	Thymus	Thymus
35	chr4:88266600-88288200	Weak transcription	Brain Germinal Matrix	brain
36	chr4:88267200-88281400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr4:88267400-88278000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr4:88267400-88278000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:88267400-88290600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:88267400-88308000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:88267600-88277000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr4:88267600-88292400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:88267800-88274800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr4:88267800-88275400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:88267800-88277800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:88267800-88306000	Weak transcription	Fetal Brain Female	brain
47	chr4:88268000-88274800	Weak transcription	Fetal Stomach	stomach
48	chr4:88268000-88275000	Weak transcription	Fetal Thymus	thymus
49	chr4:88268000-88275600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:88268000-88277000	Weak transcription	Primary T cells from cord blood	blood

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