Variant report

Variant	rs2249950
Chromosome Location	chr11:105891599-105891600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:105890839..105893464-chr11:105945938..105948303,3	K562	blood:
2	chr11:105889161..105891873-chr11:105905739..105908182,2	K562	blood:
3	chr11:105889494..105894632-chr11:105945234..105949346,5	K562	blood:

Variant related genes	Relation type
ENSG00000182359	Chromatin interaction
ENSG00000149313	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10895892	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10895893	0.81[ASN][1000 genomes]
rs10895898	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs11226894	0.81[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs11226896	0.81[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12293460	0.89[ASN][1000 genomes]
rs1939810	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2155344	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236663	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2564912	0.90[ASN][1000 genomes]
rs2564913	0.91[ASN][1000 genomes]
rs2846220	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2846221	0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2847181	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3737347	0.89[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs7952626	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv527285	chr11:105884085-105891599	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv526898	chr11:105884085-105893494	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2249950	GUCY1A2	cis	cerebellum	SCAN
rs2249950	C11orf70	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105864000-105891600	Weak transcription	Colonic Mucosa	Colon
2	chr11:105865200-105891600	Weak transcription	Hela-S3	cervix
3	chr11:105871000-105892200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:105877600-105892400	Weak transcription	Spleen	Spleen
5	chr11:105877800-105892400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:105878600-105892400	Weak transcription	Stomach Mucosa	stomach
7	chr11:105880600-105891600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:105880800-105891600	Weak transcription	Fetal Intestine Small	intestine
9	chr11:105880800-105892400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:105881400-105892000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr11:105881600-105891600	Weak transcription	Fetal Intestine Large	intestine
12	chr11:105881600-105891800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:105881600-105892000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:105881800-105891600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:105881800-105891800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:105881800-105892000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:105882000-105891800	Weak transcription	Primary B cells from cord blood	blood
18	chr11:105882000-105891800	Weak transcription	Thymus	Thymus
19	chr11:105882000-105892000	Weak transcription	Aorta	Aorta
20	chr11:105882200-105891600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr11:105882200-105891800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:105882200-105891800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:105882200-105892000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:105882200-105892400	Weak transcription	Gastric	stomach
25	chr11:105882200-105892400	Weak transcription	Lung	lung
26	chr11:105882400-105891600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:105882400-105891800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr11:105882400-105891800	Weak transcription	Fetal Muscle Leg	muscle
29	chr11:105882400-105892200	Weak transcription	Placenta	Placenta
30	chr11:105882600-105891800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr11:105883600-105891800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr11:105883800-105891600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:105883800-105891600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:105883800-105892000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:105883800-105892400	Weak transcription	Esophagus	oesophagus
36	chr11:105884000-105891600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr11:105884000-105892000	Weak transcription	Fetal Thymus	thymus
38	chr11:105884200-105891600	Weak transcription	Osteobl	bone
39	chr11:105884400-105891600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:105884400-105891800	Weak transcription	HSMM	muscle
41	chr11:105884400-105891800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr11:105884400-105892200	Weak transcription	Left Ventricle	heart
43	chr11:105885600-105891600	Weak transcription	Liver	Liver
44	chr11:105885600-105891800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr11:105886800-105891600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:105887000-105892000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr11:105888600-105892000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:105889000-105891800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr11:105889000-105892000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr11:105889000-105892200	Enhancers	Primary T helper cells fromperipheralblood	blood

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