Variant report

Variant	rs11038668
Chromosome Location	chr11:45838926-45838927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45836782..45839612-chr11:45867458..45870636,4	MCF-7	breast:
2	chr11:45837750..45841192-chr11:45868831..45870857,3	MCF-7	breast:
3	chr11:45837232..45839934-chr11:45842707..45845074,2	K562	blood:
4	chr11:45838111..45839988-chr11:45841700..45845472,4	K562	blood:
5	chr11:45833466..45835015-chr11:45838318..45840178,2	K562	blood:

Variant related genes	Relation type
ENSG00000121671	Chromatin interaction
ENSG00000255447	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10462026	0.90[EUR][1000 genomes]
rs10838519	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs10838526	0.89[EUR][1000 genomes]
rs11038670	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11038671	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11038675	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038679	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11038680	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11038683	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11038685	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11038686	0.90[EUR][1000 genomes]
rs11038689	0.90[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs11038699	0.91[GIH][hapmap]
rs12364060	0.80[CEU][hapmap]
rs1401417	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs17787106	0.89[EUR][1000 genomes]
rs17787136	0.90[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4756026	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs4756029	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4756030	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756032	0.90[EUR][1000 genomes]
rs4756036	0.90[EUR][1000 genomes]
rs55923741	0.90[EUR][1000 genomes]
rs56152508	0.90[EUR][1000 genomes]
rs56330140	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7121775	0.90[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs7123390	0.95[GIH][hapmap];0.84[TSI][hapmap]
rs72900638	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72900650	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72900652	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72900692	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72900694	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72902412	0.90[EUR][1000 genomes]
rs72902436	0.90[EUR][1000 genomes]
rs72902439	0.89[EUR][1000 genomes]
rs7949978	0.82[YRI][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	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv897315	chr11:45817637-45838926	Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11038668	OR4C45	cis	cerebellum	SCAN
rs11038668	CRY2	cis	cerebellum	SCAN
rs11038668	MAPK8IP1	cis	Whole Blood	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45832200-45839600	Weak transcription	Fetal Heart	heart
2	chr11:45833600-45848000	Weak transcription	Right Ventricle	heart
3	chr11:45833800-45841800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr11:45833800-45845400	Weak transcription	Ovary	ovary
5	chr11:45833800-45850000	Weak transcription	Brain Angular Gyrus	brain
6	chr11:45834000-45845400	Weak transcription	Fetal Intestine Large	intestine
7	chr11:45834000-45845400	Weak transcription	Left Ventricle	heart
8	chr11:45834200-45839000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:45834200-45839000	Weak transcription	Spleen	Spleen
10	chr11:45834200-45839200	Weak transcription	Adipose Nuclei	Adipose
11	chr11:45834400-45839200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:45834400-45845000	Weak transcription	Fetal Lung	lung
13	chr11:45834400-45845400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:45834400-45845600	Weak transcription	Gastric	stomach
15	chr11:45834600-45839600	Weak transcription	Placenta	Placenta
16	chr11:45834600-45845400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr11:45834600-45845400	Weak transcription	Lung	lung
18	chr11:45835000-45843200	Weak transcription	K562	blood
19	chr11:45835000-45844600	Weak transcription	Fetal Intestine Small	intestine
20	chr11:45835000-45845400	Weak transcription	Dnd41	blood
21	chr11:45837200-45839000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr11:45837200-45839600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr11:45837600-45845400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr11:45837600-45845400	Weak transcription	Fetal Kidney	kidney
25	chr11:45837600-45848200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:45838000-45845400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:45838200-45839800	Enhancers	GM12878-XiMat	blood
28	chr11:45838200-45841200	Enhancers	Primary B cells from peripheral blood	blood
29	chr11:45838400-45839400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:45838400-45841200	Weak transcription	Fetal Muscle Leg	muscle
31	chr11:45838600-45840800	Enhancers	Primary B cells from cord blood	blood
32	chr11:45838800-45839000	Enhancers	Colonic Mucosa	Colon

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