Variant report

Variant	rs2420388
Chromosome Location	chr11:34490537-34490538
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	chr11:34488557..34490555-chr11:34492029..34493917,3	K562	blood:
2	chr11:34485197..34487373-chr11:34489814..34492260,2	K562	blood:

Variant related genes	Relation type
ENSG00000121691	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10836244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076556	0.96[GIH][hapmap]
rs208681	0.85[GIH][hapmap]
rs208682	0.85[GIH][hapmap]
rs208683	0.85[GIH][hapmap]
rs2284365	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2284367	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2300182	0.92[GIH][hapmap]
rs3758733	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3781711	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4755372	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4755373	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756148	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756153	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs480575	0.83[TSI][hapmap]
rs482322	0.83[TSI][hapmap]
rs484214	0.83[TSI][hapmap]
rs524154	0.83[TSI][hapmap]
rs525938	0.83[TSI][hapmap]
rs554576	0.83[ASN][1000 genomes]
rs566979	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs6484722	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102889	0.88[GIH][hapmap]
rs7113917	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769217	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928213	0.89[ASN][1000 genomes]
rs942222	0.88[GIH][hapmap]
rs942223	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2420388	CAT	cis	Artery Tibial	GTEx
rs2420388	CAT	cis	parietal	SCAN
rs2420388	CAT	cis	multi-tissue	Pritchard
rs2420388	CAT	Cis_1M	lymphoblastoid	RTeQTL
rs2420388	CAT	cis	lymphoblastoid	seeQTL
rs2420388	CAT	cis	cerebellum	SCAN
rs2420388	CAT	cis	Whole Blood	GTEx
rs2420388	TRAF6	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34470800-34494200	Strong transcription	Brain Germinal Matrix	brain
2	chr11:34470800-34495600	Strong transcription	Stomach Smooth Muscle	stomach
3	chr11:34471000-34494000	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr11:34471400-34494000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:34471400-34494600	Strong transcription	Placenta	Placenta
6	chr11:34471400-34495000	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr11:34471400-34496400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:34471600-34495200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:34471600-34496800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr11:34474000-34496800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr11:34476200-34495200	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr11:34477200-34495200	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:34478200-34492800	Strong transcription	Rectal Smooth Muscle	rectum
14	chr11:34482400-34494200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr11:34482400-34495000	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr11:34483400-34501600	Weak transcription	HMEC	breast
17	chr11:34484600-34491400	Strong transcription	Fetal Brain Male	brain
18	chr11:34485400-34490600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:34487200-34490600	ZNF genes & repeats	Fetal Lung	lung
20	chr11:34487400-34494200	Strong transcription	NH-A	brain
21	chr11:34487600-34490600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:34487800-34490600	Weak transcription	Colonic Mucosa	Colon
23	chr11:34487800-34493800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr11:34487800-34494000	Strong transcription	HSMM	muscle
25	chr11:34487800-34494000	Strong transcription	Osteobl	bone
26	chr11:34487800-34494200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr11:34487800-34494200	Weak transcription	Brain Angular Gyrus	brain
28	chr11:34487800-34495000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:34487800-34496600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr11:34487800-34496600	Strong transcription	Hela-S3	cervix
31	chr11:34487800-34497000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr11:34488000-34492400	Weak transcription	Stomach Mucosa	stomach
33	chr11:34488000-34496400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr11:34488600-34494000	Strong transcription	NHDF-Ad	bronchial
35	chr11:34488800-34492000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:34488800-34495200	Strong transcription	Ovary	ovary
37	chr11:34489000-34493200	Strong transcription	NHLF	lung
38	chr11:34489000-34494400	Strong transcription	Fetal Intestine Large	intestine
39	chr11:34489000-34495200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:34489200-34493000	Strong transcription	K562	blood
41	chr11:34489200-34494800	Strong transcription	Primary hematopoietic stem cells	blood
42	chr11:34489200-34495200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:34489200-34495600	Strong transcription	Primary B cells from cord blood	blood
44	chr11:34489400-34494600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr11:34489400-34494800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:34489400-34495200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:34489400-34496400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:34489400-34496600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:34489400-34496800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:34489600-34493200	Strong transcription	Fetal Kidney	kidney

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