Variant report

Variant	rs11679046
Chromosome Location	chr2:234258101-234258102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234248205..234248729-chr2:234257674..234258176,2	MCF-7	breast:
2	chr2:234257933..234260937-chr2:234261415..234264229,3	K562	blood:
3	chr2:234247812..234248755-chr2:234257486..234258176,3	MCF-7	breast:
4	chr2:234255807..234258253-chr2:234261320..234263742,3	MCF-7	breast:
5	chr2:234243954..234247958-chr2:234256896..234259564,3	MCF-7	breast:
6	chr2:234196279..234198158-chr2:234258001..234260532,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259793	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000243637	Chromatin interaction
ENSG00000251791	Chromatin interaction
ENSG00000130561	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1000141	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs1046974	0.89[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10803624	0.95[ASN][1000 genomes]
rs10803625	0.82[ASN][1000 genomes]
rs11676156	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11681192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002340	0.83[ASN][1000 genomes]
rs13003198	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13014016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2241873	0.82[CHB][hapmap]
rs2289477	0.81[CHB][hapmap]
rs2879924	0.95[ASN][1000 genomes]
rs2879925	0.94[ASN][1000 genomes]
rs34595600	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34891595	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35480652	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828305	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs67399374	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6756706	0.83[CHB][hapmap]
rs7423426	0.95[ASN][1000 genomes]
rs880114	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs880116	0.95[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11679046	ECEL1	cis	multi-tissue	Pritchard
rs11679046	ATG16L1	cis	cerebellum	SCAN
rs11679046	SLC16A14	cis	cerebellum	SCAN
rs11679046	SAG	cis	multi-tissue	Pritchard
rs11679046	DGKD	cis	lymphoblastoid	seeQTL
rs11679046	SCARNA5	cis	cerebellum	SCAN
rs11679046	SCARNA5	cis	parietal	SCAN
rs11679046	DGKD	cis	cerebellum	SCAN
rs11679046	LRRC55	trans	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234255000-234260000	Enhancers	Liver	Liver
2	chr2:234255600-234258600	Enhancers	Brain Substantia Nigra	brain
3	chr2:234255800-234258600	Flanking Active TSS	HepG2	liver
4	chr2:234255800-234262400	Weak transcription	Right Atrium	heart
5	chr2:234256200-234260800	Enhancers	Primary B cells from peripheral blood	blood
6	chr2:234256400-234260400	Enhancers	Fetal Intestine Small	intestine
7	chr2:234256400-234262400	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr2:234256600-234259800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:234256600-234261400	Enhancers	Primary B cells from cord blood	blood
10	chr2:234256800-234258400	Enhancers	Gastric	stomach
11	chr2:234256800-234258800	Enhancers	Brain Angular Gyrus	brain
12	chr2:234256800-234262400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr2:234257000-234258800	Enhancers	Fetal Muscle Trunk	muscle
14	chr2:234257000-234259200	Enhancers	Fetal Muscle Leg	muscle
15	chr2:234257000-234262200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:234257200-234259400	Enhancers	Fetal Thymus	thymus
17	chr2:234257200-234260000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr2:234257200-234260400	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:234257400-234258200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr2:234257400-234258400	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr2:234257400-234258400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr2:234257400-234258600	Enhancers	Placenta	Placenta
23	chr2:234257400-234258600	Enhancers	Spleen	Spleen
24	chr2:234257400-234258800	Weak transcription	Small Intestine	intestine
25	chr2:234257400-234260400	Enhancers	Fetal Intestine Large	intestine
26	chr2:234257600-234258200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:234257600-234258200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:234257600-234258200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:234257600-234258200	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr2:234257600-234258200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:234257600-234258200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr2:234257600-234258200	Enhancers	Lung	lung
33	chr2:234257600-234258200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr2:234257600-234258200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
35	chr2:234257600-234258400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:234257600-234258400	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr2:234257600-234258400	Enhancers	Thymus	Thymus
38	chr2:234257600-234258400	Enhancers	HSMMtube	muscle
39	chr2:234257600-234258600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr2:234257600-234259000	Enhancers	A549	lung
41	chr2:234257600-234260000	Enhancers	Stomach Mucosa	stomach
42	chr2:234257600-234260400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:234257800-234258200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr2:234257800-234258200	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr2:234257800-234258200	Enhancers	Psoas Muscle	Psoas
46	chr2:234257800-234258200	Enhancers	Right Ventricle	heart
47	chr2:234257800-234258200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr2:234257800-234258400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:234257800-234258400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr2:234257800-234258600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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