Variant report

Variant	rs2138767
Chromosome Location	chr11:47629793-47629794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47607110..47610059-chr11:47627061..47630837,3	K562	blood:
2	chr11:47620964..47622605-chr11:47627405..47629892,2	MCF-7	breast:
3	chr11:47628108..47630703-chr11:47631634..47634626,3	K562	blood:
4	chr11:47628145..47629992-chr11:47630122..47633055,2	MCF-7	breast:
5	chr11:47614458..47617193-chr11:47629185..47630733,2	K562	blood:
6	chr11:47627983..47630476-chr11:47633126..47635278,2	K562	blood:

Variant related genes	Relation type
ENSG00000196666	Chromatin interaction
ENSG00000172247	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1044269	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs10742805	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs10742806	0.94[JPT][hapmap]
rs10742816	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039300	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11039387	0.81[ASN][1000 genomes]
rs11819955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11819979	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11820480	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12419342	0.94[JPT][hapmap]
rs1474056	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17198158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs17790804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17791016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2242511	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2305982	0.81[ASN][1000 genomes]
rs2305983	0.81[ASN][1000 genomes]
rs2869531	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2869532	0.88[ASN][1000 genomes]
rs3740684	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs3824867	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs3847503	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap]
rs4147730	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4237544	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4282946	0.94[JPT][hapmap]
rs4752783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs4752786	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4752837	0.94[JPT][hapmap]
rs4752839	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap]
rs4752842	0.82[MEX][hapmap]
rs4752843	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs4752848	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4752871	0.81[ASN][1000 genomes]
rs4752872	0.81[ASN][1000 genomes]
rs4752877	0.81[ASN][1000 genomes]
rs57436966	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57828885	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58119589	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58357937	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59205786	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59837204	0.84[EUR][1000 genomes]
rs60515486	0.86[ASN][1000 genomes]
rs6485772	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6485774	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6485783	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs6485784	0.81[ASN][1000 genomes]
rs6485788	0.81[ASN][1000 genomes]
rs7105122	0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap]
rs7105907	0.94[JPT][hapmap]
rs7111873	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7116299	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7121264	0.86[ASN][1000 genomes]
rs7124949	0.81[ASN][1000 genomes]
rs7126210	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs753812	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.81[YRI][hapmap]
rs7927611	0.81[ASN][1000 genomes]
rs7931089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7942031	0.81[ASN][1000 genomes]
rs7944532	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7945911	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7948705	0.94[JPT][hapmap]
rs7952204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9666924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][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	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2138767	SLC35C1	cis	cerebellum	SCAN
rs2138767	LOC441601	cis	cerebellum	SCAN
rs2138767	ATG13	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47607000-47632800	Weak transcription	Dnd41	blood
2	chr11:47616600-47631400	Weak transcription	Spleen	Spleen
3	chr11:47616600-47632400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:47616600-47632600	Weak transcription	Brain Substantia Nigra	brain
5	chr11:47617600-47643200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:47617800-47632400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr11:47618000-47639200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:47619400-47631400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:47619600-47631400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:47619600-47631600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr11:47620800-47637800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:47621000-47640400	Weak transcription	Fetal Brain Female	brain
13	chr11:47621600-47632400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:47621600-47638200	Weak transcription	Hela-S3	cervix
15	chr11:47621600-47647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:47621800-47631400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:47621800-47632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:47621800-47642000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:47622000-47636000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:47622000-47637600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:47623000-47632800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:47623800-47632400	Weak transcription	Gastric	stomach
23	chr11:47624200-47631400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr11:47624200-47632600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:47624400-47632400	Weak transcription	Fetal Thymus	thymus
26	chr11:47625200-47632600	Weak transcription	Primary B cells from cord blood	blood
27	chr11:47625200-47637800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr11:47626000-47632800	Weak transcription	Psoas Muscle	Psoas
29	chr11:47626000-47638400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:47626200-47631400	Weak transcription	Fetal Intestine Large	intestine
31	chr11:47626200-47638400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr11:47626400-47631200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr11:47626400-47631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:47626400-47639200	Weak transcription	Colonic Mucosa	Colon
35	chr11:47626600-47635000	Weak transcription	A549	lung
36	chr11:47626600-47639000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr11:47627000-47630400	Enhancers	Fetal Heart	heart
38	chr11:47627600-47629800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr11:47627600-47630000	Enhancers	Osteobl	bone
40	chr11:47627600-47630200	Enhancers	NH-A	brain
41	chr11:47627800-47631200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr11:47627800-47643200	Weak transcription	Pancreas	Pancrea
43	chr11:47628000-47630000	Enhancers	Brain Hippocampus Middle	brain
44	chr11:47628000-47630200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:47628200-47629800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:47628200-47629800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:47628200-47629800	Enhancers	Right Atrium	heart
48	chr11:47628200-47630000	Enhancers	Adipose Nuclei	Adipose
49	chr11:47628200-47630000	Strong transcription	Thymus	Thymus
50	chr11:47628200-47630200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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