Variant report

Variant	rs13196280
Chromosome Location	chr6:110085366-110085367
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11964533	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11964864	0.91[EUR][1000 genomes]
rs11968978	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12526189	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12661287	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13191444	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194387	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13197056	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198879	0.91[EUR][1000 genomes]
rs13203636	0.99[ASN][1000 genomes]
rs13207864	0.84[EUR][1000 genomes]
rs13211604	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13212535	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv886533	chr6:110067773-110126393	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13196280	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs13196280	SMPD2	cis	Whole Blood	GTEx
rs13196280	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
2	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
4	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
5	chr6:110042200-110088800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:110042400-110089000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
8	chr6:110048600-110089800	Weak transcription	Fetal Kidney	kidney
9	chr6:110057200-110089000	Weak transcription	Fetal Brain Female	brain
10	chr6:110057400-110089000	Weak transcription	Esophagus	oesophagus
11	chr6:110057600-110086200	Weak transcription	Brain Anterior Caudate	brain
12	chr6:110058200-110087200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:110058200-110089000	Weak transcription	Lung	lung
14	chr6:110058400-110089600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:110058800-110112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:110059200-110124000	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:110060000-110087800	Weak transcription	Fetal Thymus	thymus
18	chr6:110061200-110089200	Weak transcription	Pancreas	Pancrea
19	chr6:110062600-110089200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:110062800-110087400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:110062800-110088000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:110065200-110089000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:110065200-110111200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:110065400-110094200	Weak transcription	Brain Substantia Nigra	brain
25	chr6:110065600-110087200	Weak transcription	HSMMtube	muscle
26	chr6:110065600-110087400	Weak transcription	Fetal Stomach	stomach
27	chr6:110065600-110089000	Weak transcription	Gastric	stomach
28	chr6:110065600-110089200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:110065800-110086200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:110065800-110086400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:110065800-110087200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:110065800-110087200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:110065800-110088600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:110065800-110089000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:110065800-110089000	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:110065800-110089000	Weak transcription	Thymus	Thymus
37	chr6:110065800-110107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:110065800-110107400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:110066000-110087200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:110067800-110089000	Weak transcription	Fetal Lung	lung
41	chr6:110069400-110086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:110069800-110089200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:110070200-110087200	Weak transcription	Adipose Nuclei	Adipose
44	chr6:110070200-110089000	Weak transcription	Aorta	Aorta
45	chr6:110072000-110089000	Weak transcription	Ovary	ovary
46	chr6:110076600-110089000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:110078200-110089000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:110078600-110088000	Weak transcription	NHDF-Ad	bronchial
49	chr6:110078800-110107400	Weak transcription	Fetal Brain Male	brain
50	chr6:110079600-110088600	Weak transcription	Fetal Muscle Leg	muscle

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