Variant report

Variant	rs13194387
Chromosome Location	chr6:110066935-110066936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11964533	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11964864	0.88[EUR][1000 genomes]
rs11968978	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12526189	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12661287	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13191444	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196280	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13197056	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198879	0.88[EUR][1000 genomes]
rs13203636	0.99[ASN][1000 genomes]
rs13207864	0.81[EUR][1000 genomes]
rs13211604	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13212535	0.85[AMR][1000 genomes];0.82[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	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv5436	chr6:110052812-110097662	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13194387	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs13194387	SMPD2	cis	Whole Blood	GTEx
rs13194387	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs13194387	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
2	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
6	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
8	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
9	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
10	chr6:110039000-110081000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:110041400-110081000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:110042200-110088800	Weak transcription	Fetal Intestine Small	intestine
13	chr6:110042400-110089000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
15	chr6:110047000-110067200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:110047200-110084000	Weak transcription	Small Intestine	intestine
17	chr6:110047600-110068800	Weak transcription	Dnd41	blood
18	chr6:110048600-110089800	Weak transcription	Fetal Kidney	kidney
19	chr6:110050400-110078400	Weak transcription	Fetal Brain Male	brain
20	chr6:110056800-110067400	Weak transcription	Fetal Lung	lung
21	chr6:110057200-110089000	Weak transcription	Fetal Brain Female	brain
22	chr6:110057400-110089000	Weak transcription	Esophagus	oesophagus
23	chr6:110057600-110086200	Weak transcription	Brain Anterior Caudate	brain
24	chr6:110058200-110087200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:110058200-110089000	Weak transcription	Lung	lung
26	chr6:110058400-110085000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:110058400-110089600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:110058800-110112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:110059200-110067000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:110059200-110069400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:110059200-110124000	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:110060000-110087800	Weak transcription	Fetal Thymus	thymus
33	chr6:110060400-110068000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:110061200-110089200	Weak transcription	Pancreas	Pancrea
35	chr6:110062400-110067200	Weak transcription	Psoas Muscle	Psoas
36	chr6:110062600-110089200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:110062800-110087400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:110062800-110088000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:110063000-110078000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:110065200-110084000	Weak transcription	Left Ventricle	heart
41	chr6:110065200-110089000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:110065200-110111200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:110065400-110094200	Weak transcription	Brain Substantia Nigra	brain
44	chr6:110065600-110067400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:110065600-110067600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:110065600-110067600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr6:110065600-110067800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:110065600-110068200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:110065600-110069000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:110065600-110069200	Weak transcription	Aorta	Aorta

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