Variant report

Variant	rs4938869
Chromosome Location	chr11:57291801-57291802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57259469..57263127-chr11:57289484..57293312,4	K562	blood:
2	chr11:57289789..57291909-chr11:57295120..57298290,3	K562	blood:
3	chr11:57280522..57282565-chr11:57289754..57292576,2	K562	blood:
4	chr11:57265588..57267157-chr11:57289591..57291810,2	K562	blood:

Variant related genes	Relation type
ENSG00000149150	Chromatin interaction
ENSG00000134809	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10160419	0.88[JPT][hapmap]
rs10792101	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792104	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10792106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10792107	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10896623	0.89[ASW][hapmap]
rs1115172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs11229057	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12275916	0.88[JPT][hapmap]
rs2508443	0.82[CHB][hapmap]
rs35253626	0.82[ASN][1000 genomes]
rs3891975	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4938871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4938873	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4939146	0.88[JPT][hapmap]
rs4939148	0.89[ASW][hapmap]
rs4939149	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939151	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4939152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4939153	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61886997	0.91[ASN][1000 genomes]
rs6591429	0.88[JPT][hapmap]
rs7101425	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112126	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7123582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7124330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7128015	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7131076	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7933797	0.88[JPT][hapmap]
rs7934626	0.88[JPT][hapmap]
rs7940223	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7950126	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription 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 miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1051032	chr11:57290124-57363064	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv541049	chr11:57290124-57363064	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4938869	SMTNL1	cis	lymphoblastoid	seeQTL
rs4938869	TIMM10	cis	parietal	SCAN
rs4938869	LPXN	cis	parietal	SCAN
rs4938869	BHLHE40	trans	cerebellum	SCAN
rs4938869	CLP1	cis	cerebellum	SCAN
rs4938869	OR5M10	cis	cerebellum	SCAN
rs4938869	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs4938869	MS4A13	cis	cerebellum	SCAN
rs4938869	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs4938869	OR5J2	cis	parietal	SCAN
rs4938869	TIMM10	cis	lung	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57283400-57297400	Weak transcription	Gastric	stomach
2	chr11:57283600-57292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:57283600-57292400	Weak transcription	Aorta	Aorta
4	chr11:57283600-57295200	Weak transcription	Lung	lung
5	chr11:57283600-57296000	Weak transcription	Spleen	Spleen
6	chr11:57283600-57296200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:57283800-57292200	Weak transcription	Brain Hippocampus Middle	brain
8	chr11:57283800-57292200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:57283800-57292200	Weak transcription	Brain Substantia Nigra	brain
10	chr11:57283800-57292200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:57283800-57292400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:57283800-57292400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:57283800-57292400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:57283800-57293800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:57283800-57293800	Weak transcription	HUVEC	blood vessel
16	chr11:57283800-57294400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:57283800-57294400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:57283800-57294600	Weak transcription	Primary T cells from cord blood	blood
19	chr11:57283800-57295000	Weak transcription	NHLF	lung
20	chr11:57283800-57295000	Weak transcription	Osteobl	bone
21	chr11:57283800-57295200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:57283800-57295200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:57283800-57295200	Weak transcription	Brain Anterior Caudate	brain
24	chr11:57283800-57295200	Weak transcription	Fetal Intestine Small	intestine
25	chr11:57283800-57295200	Weak transcription	Fetal Muscle Leg	muscle
26	chr11:57283800-57295800	Weak transcription	Fetal Intestine Large	intestine
27	chr11:57283800-57296000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:57283800-57296000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:57283800-57296000	Weak transcription	Left Ventricle	heart
30	chr11:57283800-57296200	Weak transcription	HSMM	muscle
31	chr11:57283800-57296400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:57283800-57296600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:57283800-57296600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:57283800-57297000	Weak transcription	Brain Angular Gyrus	brain
35	chr11:57283800-57297200	Weak transcription	Fetal Lung	lung
36	chr11:57283800-57297200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr11:57283800-57297200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr11:57283800-57297200	Weak transcription	Right Atrium	heart
39	chr11:57283800-57297200	Weak transcription	NH-A	brain
40	chr11:57283800-57297400	Weak transcription	Colonic Mucosa	Colon
41	chr11:57283800-57297400	Weak transcription	HSMMtube	muscle
42	chr11:57284000-57292200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:57284000-57292200	Weak transcription	A549	lung
44	chr11:57284000-57292400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:57284000-57294000	Weak transcription	GM12878-XiMat	blood
46	chr11:57284000-57294200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr11:57284000-57294600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr11:57284000-57295800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr11:57284000-57296000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:57284000-57296000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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