Variant report

Variant	rs138685
Chromosome Location	chr22:28469630-28469631
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	chr22:28464126..28466768-chr22:28468143..28470001,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs118839	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12171034	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs138631	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs138638	0.93[CHD][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs138650	0.87[ASW][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs138657	0.92[CEU][hapmap]
rs138675	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs138683	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs138684	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1548235	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2038158	0.88[ASN][1000 genomes]
rs2092054	0.81[ASN][1000 genomes]
rs3747141	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[TSI][hapmap]
rs4140571	0.82[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs470100	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs470105	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752667	0.86[ASN][1000 genomes]
rs5762418	0.84[ASN][1000 genomes]
rs6005671	0.81[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap]
rs720621	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs73425788	0.84[ASN][1000 genomes]
rs738451	0.82[CHD][hapmap];0.84[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs138685	ARG2	trans	parietal	SCAN
rs138685	TTC28	cis	lymphoblastoid	seeQTL
rs138685	TTC28AS	cis	cerebellum	SCAN
rs138685	ZNF280A	cis	cerebellum	SCAN
rs138685	SEZ6L	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28445200-28470400	Weak transcription	Pancreas	Pancrea
2	chr22:28445400-28470800	Weak transcription	Lung	lung
3	chr22:28449600-28479200	Weak transcription	Brain Germinal Matrix	brain
4	chr22:28449600-28488200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr22:28450000-28471400	Weak transcription	Colon Smooth Muscle	Colon
6	chr22:28456800-28471400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr22:28457400-28471400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:28458400-28471200	Weak transcription	Small Intestine	intestine
9	chr22:28459400-28471200	Weak transcription	Brain Anterior Caudate	brain
10	chr22:28459600-28471400	Weak transcription	HepG2	liver
11	chr22:28460000-28471200	Weak transcription	Aorta	Aorta
12	chr22:28461600-28470800	Weak transcription	Right Ventricle	heart
13	chr22:28461600-28471200	Weak transcription	Ovary	ovary
14	chr22:28462000-28471200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr22:28463000-28470400	Weak transcription	Left Ventricle	heart
16	chr22:28463000-28471400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr22:28465400-28471200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr22:28465400-28471200	Weak transcription	HSMMtube	muscle
19	chr22:28465800-28471400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr22:28466000-28470600	Weak transcription	Osteobl	bone
21	chr22:28466000-28471600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr22:28466200-28471800	Strong transcription	Dnd41	blood
23	chr22:28466400-28471200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr22:28466400-28471200	Weak transcription	NHLF	lung
25	chr22:28466400-28489800	Weak transcription	Fetal Brain Male	brain
26	chr22:28466600-28503600	Weak transcription	Hela-S3	cervix
27	chr22:28467400-28470400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr22:28467400-28470400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr22:28467600-28470000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:28467800-28470000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr22:28467800-28470600	Strong transcription	Fetal Muscle Leg	muscle
32	chr22:28467800-28470800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr22:28467800-28471200	Weak transcription	Brain Substantia Nigra	brain
34	chr22:28468000-28470000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr22:28468000-28471000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr22:28468000-28471200	Strong transcription	Fetal Stomach	stomach
37	chr22:28468400-28470000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr22:28468400-28471200	Weak transcription	Fetal Lung	lung
39	chr22:28468400-28471200	Weak transcription	NHDF-Ad	bronchial
40	chr22:28468600-28470000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr22:28468600-28471200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr22:28468600-28477200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr22:28468600-28489800	Weak transcription	Fetal Kidney	kidney
44	chr22:28468800-28470400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr22:28468800-28480000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr22:28469000-28470400	Weak transcription	Fetal Intestine Large	intestine
47	chr22:28469000-28470400	Weak transcription	Fetal Intestine Small	intestine
48	chr22:28469000-28470400	Weak transcription	Gastric	stomach
49	chr22:28469000-28470600	Weak transcription	Adipose Nuclei	Adipose
50	chr22:28469000-28471200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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