Variant report

Variant	rs336277
Chromosome Location	chr18:29640430-29640431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29637884..29642506-chr18:29670649..29674281,4	K562	blood:

Variant related genes	Relation type
ENSG00000265008	Chromatin interaction
ENSG00000134758	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12455805	0.85[JPT][hapmap]
rs170861	0.81[ASN][1000 genomes]
rs2432699	0.82[ASN][1000 genomes]
rs2901365	0.81[JPT][hapmap]
rs336273	0.86[ASN][1000 genomes]
rs336275	0.81[JPT][hapmap]
rs336279	0.81[CHB][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs336280	0.82[ASN][1000 genomes]
rs336281	0.88[MEX][hapmap]
rs8086733	0.88[MEX][hapmap]
rs9946075	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9947278	0.81[JPT][hapmap]

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	esv1803283	chr18:29591102-29640430	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
2	nsv1061305	chr18:29609935-29664528	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv2757673	chr18:29632749-29674992	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2758719	chr18:29632749-29674992	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1064505	chr18:29637586-29659148	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs336277	MCART2	cis	parietal	SCAN
rs336277	DSG1	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29602600-29664200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr18:29604600-29656000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr18:29615200-29648400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr18:29618400-29646800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr18:29618600-29642800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr18:29619400-29645400	Weak transcription	Fetal Stomach	stomach
7	chr18:29626000-29657200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr18:29630000-29646600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr18:29630000-29664400	Weak transcription	Fetal Muscle Leg	muscle
10	chr18:29630200-29646400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr18:29630400-29646600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr18:29630400-29650800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:29630400-29664400	Weak transcription	Left Ventricle	heart
14	chr18:29630800-29641800	Weak transcription	Primary B cells from cord blood	blood
15	chr18:29630800-29658600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr18:29631200-29640800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr18:29631400-29671400	Weak transcription	Hela-S3	cervix
18	chr18:29635200-29650600	Weak transcription	Lung	lung
19	chr18:29635600-29644600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr18:29635600-29646400	Weak transcription	Adipose Nuclei	Adipose
21	chr18:29635600-29646600	Weak transcription	Fetal Thymus	thymus
22	chr18:29635800-29641400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr18:29637000-29646600	Weak transcription	Fetal Intestine Large	intestine
24	chr18:29637200-29646800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr18:29637800-29640600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr18:29638000-29644000	Weak transcription	Fetal Intestine Small	intestine
27	chr18:29638000-29644400	Weak transcription	Right Atrium	heart
28	chr18:29638000-29652200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr18:29638000-29652200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr18:29638600-29640600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr18:29638800-29640600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr18:29639000-29640600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr18:29639400-29640800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr18:29639600-29640600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr18:29639600-29645200	Weak transcription	Liver	Liver
36	chr18:29639800-29642200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr18:29640200-29640600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr18:29640200-29642600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr18:29640200-29643600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr18:29640200-29645800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr18:29640400-29640600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr18:29640400-29641400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr18:29640400-29641800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr18:29640400-29642400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr18:29640400-29642600	Strong transcription	Primary T cells from cord blood	blood
46	chr18:29640400-29644400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr18:29640400-29646400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr18:29640400-29651600	Weak transcription	Spleen	Spleen
49	chr18:29640400-29652400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr18:29640400-29664400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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