Variant report

Variant	rs11042439
Chromosome Location	chr11:9622254-9622255
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9620438..9623040-chr11:9627424..9629969,2	K562	blood:
2	chr11:9616144..9619684-chr11:9621223..9625658,6	K562	blood:

Variant related genes	Relation type
ENSG00000243964	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10770044	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs10840287	0.86[CEU][hapmap]
rs11042433	0.81[AMR][1000 genomes]
rs11042436	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042437	0.81[CEU][hapmap]
rs11042438	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042441	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042442	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042443	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042466	1.00[ASW][hapmap];0.91[CEU][hapmap]
rs11600183	0.86[CEU][hapmap]
rs12416887	1.00[YRI][hapmap]
rs12422111	0.95[GIH][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs12807017	0.95[CEU][hapmap];0.86[GIH][hapmap]
rs35042828	0.81[AMR][1000 genomes]
rs35084800	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36084509	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4910487	0.86[CEU][hapmap]
rs7120616	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7123263	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7928738	0.86[GIH][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11042439	OR2D2	cis	cerebellum	SCAN
rs11042439	TMEM41B	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9597200-9635000	Weak transcription	Pancreas	Pancrea
2	chr11:9599600-9622800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:9599800-9622400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:9601400-9622600	Weak transcription	Right Atrium	heart
5	chr11:9607000-9622400	Weak transcription	Small Intestine	intestine
6	chr11:9607800-9622600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:9610200-9622600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:9610600-9622600	Weak transcription	Colonic Mucosa	Colon
9	chr11:9610600-9622600	Weak transcription	Esophagus	oesophagus
10	chr11:9610600-9622600	Weak transcription	Thymus	Thymus
11	chr11:9610600-9622800	Weak transcription	Right Ventricle	heart
12	chr11:9610600-9627200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:9610600-9635000	Weak transcription	Aorta	Aorta
14	chr11:9610800-9622600	Weak transcription	Brain Germinal Matrix	brain
15	chr11:9610800-9622600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:9611000-9622600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:9611200-9622600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr11:9611200-9622600	Weak transcription	K562	blood
19	chr11:9611200-9622800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:9611400-9622600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:9611400-9623400	Weak transcription	Fetal Lung	lung
22	chr11:9611600-9622400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr11:9611600-9622600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:9611600-9622600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:9611800-9622600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:9612000-9623200	Weak transcription	Liver	Liver
27	chr11:9612200-9622600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:9612200-9622800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:9612200-9622800	Weak transcription	Fetal Intestine Small	intestine
30	chr11:9612400-9622600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:9612400-9622600	Weak transcription	Fetal Intestine Large	intestine
32	chr11:9612400-9622800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:9612600-9622600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:9612600-9623000	Weak transcription	HUVEC	blood vessel
35	chr11:9613000-9622600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr11:9616200-9622800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:9616800-9622800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:9617000-9622400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:9617200-9622400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:9617200-9622600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:9617200-9622600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr11:9617200-9622800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:9617400-9622600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:9617800-9622800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:9618800-9622600	Weak transcription	Osteobl	bone
46	chr11:9621200-9622600	Enhancers	Primary B cells from peripheral blood	blood
47	chr11:9621600-9622600	Enhancers	Primary hematopoietic stem cells	blood
48	chr11:9621800-9622400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:9621800-9622400	Enhancers	Dnd41	blood
50	chr11:9621800-9622600	Enhancers	Primary T cells fromperipheralblood	blood

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