Variant report

Variant	rs7933164
Chromosome Location	chr11:4093950-4093951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr11:4093841-4094406	A549	lung:	n/a	chr11:4094103-4094122
2	SMC3	chr11:4093823-4094323	HepG2	liver:	n/a	chr11:4094107-4094121
3	ATF1	chr11:4093914-4094192	K562	blood:	n/a	n/a
4	CTCF	chr11:4093897-4094186	T-47D	breast:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
5	CTCF	chr11:4093934-4094281	A549	lung:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
6	CTCF	chr11:4093896-4094235	MCF-7	breast:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
7	SMC3	chr11:4093540-4094327	Hela-S3	cervix:	n/a	chr11:4094107-4094121
8	MAFF	chr11:4093885-4094161	K562	blood:	n/a	n/a
9	RCOR1	chr11:4093902-4094265	K562	blood:	n/a	n/a
10	RAD21	chr11:4093796-4094375	MCF-7	breast:	n/a	chr11:4094103-4094122
11	CTCF	chr11:4093897-4094247	A549	lung:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
12	MYC	chr11:4093936-4094247	K562	blood:	n/a	n/a
13	CTCF	chr11:4093933-4094254	H1-hESC	embryonic stem cell:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
14	MAZ	chr11:4093874-4094283	K562	blood:	n/a	n/a
15	YY1	chr11:4093886-4094237	K562	blood:	n/a	n/a
16	MYC	chr11:4093908-4094206	MCF10A-Er-Src	breast:	n/a	n/a
17	YY1	chr11:4093946-4094226	K562	blood:	n/a	n/a
18	YY1	chr11:4093909-4094296	GM12891	blood:	n/a	n/a
19	RCOR1	chr11:4093851-4094205	K562	blood:	n/a	n/a
20	CTCF	chr11:4093013-4094523	SK-N-SH	brain:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4093512-4093522 chr11:4094105-4094123 chr11:4094106-4094122
21	YY1	chr11:4093886-4094282	SK-N-SH	brain:	n/a	n/a
22	CTCF	chr11:4093646-4094501	HCT-116	colon:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
23	RAD21	chr11:4093900-4094315	K562	blood:	n/a	chr11:4094103-4094122
24	CTCF	chr11:4093827-4094314	HepG2	liver:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
25	YY1	chr11:4093908-4094234	HCT-116	colon:	n/a	n/a
26	YY1	chr11:4093827-4094292	H1-hESC	embryonic stem cell:	n/a	n/a
27	CUX1	chr11:4093741-4094265	K562	blood:	n/a	chr11:4093814-4093825 chr11:4093810-4093824
28	CTCF	chr11:4093839-4094343	A549	lung:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
29	EP300	chr11:4093896-4094204	K562	blood:	n/a	chr11:4093973-4093987
30	YY1	chr11:4093906-4094223	GM12892	blood:	n/a	n/a
31	RAD21	chr11:4093831-4094387	H1-hESC	embryonic stem cell:	n/a	chr11:4094103-4094122
32	CTCF	chr11:4093208-4094578	A549	lung:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4093512-4093522 chr11:4094105-4094123 chr11:4094106-4094122
33	CTCF	chr11:4093909-4094279	A549	lung:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
34	CTCF	chr11:4093862-4094527	IMR90	lung:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
35	YY1	chr11:4093894-4094269	A549	lung:	n/a	n/a
36	RAD21	chr11:4093334-4094528	IMR90	lung:	n/a	chr11:4094471-4094480 chr11:4094103-4094122
37	YY1	chr11:4093944-4094238	GM12878	blood:	n/a	n/a
38	YY1	chr11:4093849-4094248	SK-N-SH_RA	brain:	n/a	n/a
39	SMC3	chr11:4093780-4094297	K562	blood:	n/a	chr11:4094107-4094121
40	RAD21	chr11:4092850-4094572	SK-N-SH	brain:	n/a	chr11:4094471-4094480 chr11:4094103-4094122
41	UBTF	chr11:4093823-4094200	K562	blood:	n/a	n/a
42	MYC	chr11:4093451-4094288	NB4	blood:	n/a	chr11:4093754-4093763
43	ZNF143	chr11:4093930-4094282	K562	blood:	n/a	n/a
44	CTCF	chr11:4093946-4094317	H1-hESC	embryonic stem cell:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
45	YY1	chr11:4093668-4094302	SK-N-SH	brain:	n/a	n/a
46	RAD21	chr11:4093798-4094283	MCF-7	breast:	n/a	chr11:4094103-4094122
47	CTCF	chr11:4093877-4094164	ECC-1	luminal epithelium:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122
48	ELK1	chr11:4093857-4094215	K562	blood:	n/a	n/a
49	RAD21	chr11:4093877-4094284	GM12878	blood:	n/a	chr11:4094103-4094122
50	CTCF	chr11:4093946-4094260	SK-N-SH_RA	brain:	n/a	chr11:4094108-4094118 chr11:4094100-4094121 chr11:4094105-4094123 chr11:4094106-4094122

No.	Distal block	Cell Line	Cell type
1	chr11:3845800..3846686-chr11:4093469..4094858,7	K562	blood:
2	chr11:3828797..3829760-chr11:4093607..4094549,3	K562	blood:
3	chr11:3875831..3876713-chr11:4093611..4094184,2	MCF-7	breast:
4	chr11:3870169..3871185-chr11:4093536..4094651,4	MCF-7	breast:
5	chr11:3875802..3877279-chr11:4093389..4094585,5	K562	blood:
6	chr11:3845685..3846544-chr11:4093181..4094168,3	MCF-7	breast:
7	chr11:3870263..3871130-chr11:4093603..4094548,6	K562	blood:
8	chr11:4082609..4084818-chr11:4091785..4094735,2	K562	blood:
9	chr11:4088238..4090623-chr11:4092934..4095144,2	K562	blood:
10	chr11:3948392..3949376-chr11:4093449..4094397,2	MCF-7	breast:
11	chr11:3846755..3850440-chr11:4090727..4095329,4	K562	blood:
12	chr11:3869715..3872142-chr11:4092471..4094977,3	K562	blood:

Variant related genes	Relation type
STIM1	TF binding region
ENSG00000167323	Chromatin interaction
ENSG00000228661	Chromatin interaction
ENSG00000148985	Chromatin interaction
ENSG00000229368	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10767827	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10767828	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10835605	0.85[ASN][1000 genomes]
rs11030841	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.80[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12364664	0.90[YRI][hapmap]
rs12803023	0.90[MKK][hapmap];0.80[YRI][hapmap]
rs1372805	0.88[MKK][hapmap]
rs1561876	0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1662162	0.85[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap]
rs1735068	0.85[CHB][hapmap];0.86[GIH][hapmap]
rs2304891	0.88[MKK][hapmap]
rs2920143	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs2920144	0.84[MKK][hapmap]
rs2959068	0.90[MKK][hapmap];0.80[YRI][hapmap]
rs2959074	0.80[YRI][hapmap]
rs3794050	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4365044	0.90[CHB][hapmap]
rs4910882	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910883	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910909	0.84[CHB][hapmap]
rs6578440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6578448	0.83[CHB][hapmap]
rs7103860	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7104462	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7110060	0.90[YRI][hapmap]
rs7945532	0.84[CHB][hapmap]

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	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7933164	OR10A4	cis	parietal	SCAN
rs7933164	OR2D2	cis	cerebellum	SCAN
rs7933164	OR52A1	cis	parietal	SCAN
rs7933164	OR52I2	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4066200-4104200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:4066400-4107800	Weak transcription	Small Intestine	intestine
3	chr11:4070800-4108600	Weak transcription	HSMM	muscle
4	chr11:4076200-4103000	Weak transcription	Fetal Intestine Large	intestine
5	chr11:4079000-4112600	Weak transcription	Fetal Brain Female	brain
6	chr11:4081000-4101800	Weak transcription	Lung	lung
7	chr11:4081000-4104600	Weak transcription	Colonic Mucosa	Colon
8	chr11:4081200-4095400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:4081400-4095600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:4081800-4095200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:4081800-4095600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:4082600-4094800	Weak transcription	Spleen	Spleen
13	chr11:4082600-4107400	Weak transcription	Stomach Mucosa	stomach
14	chr11:4082800-4103400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:4083000-4094200	Weak transcription	K562	blood
16	chr11:4083000-4095000	Weak transcription	HMEC	breast
17	chr11:4083200-4102200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:4084200-4095400	Weak transcription	NHEK	skin
19	chr11:4086200-4102600	Weak transcription	Pancreas	Pancrea
20	chr11:4086200-4115200	Weak transcription	NHDF-Ad	bronchial
21	chr11:4086400-4094800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr11:4087200-4102400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:4087600-4102400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:4087600-4115000	Weak transcription	HSMMtube	muscle
25	chr11:4087800-4107800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:4088000-4101800	Weak transcription	Aorta	Aorta
27	chr11:4088600-4107800	Weak transcription	Right Ventricle	heart
28	chr11:4090400-4095000	Weak transcription	Adipose Nuclei	Adipose
29	chr11:4090400-4102800	Weak transcription	Gastric	stomach
30	chr11:4090800-4097000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr11:4090800-4097600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr11:4091000-4095400	Weak transcription	Esophagus	oesophagus
33	chr11:4091200-4097800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:4091400-4095400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:4091600-4096800	Strong transcription	Primary B cells from cord blood	blood
36	chr11:4091600-4102800	Weak transcription	Left Ventricle	heart
37	chr11:4091600-4107600	Weak transcription	Psoas Muscle	Psoas
38	chr11:4091800-4095000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr11:4091800-4101600	Weak transcription	HepG2	liver
40	chr11:4092200-4095000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:4092800-4094000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr11:4092800-4094000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr11:4092800-4094000	Enhancers	Fetal Lung	lung
44	chr11:4092800-4094000	Enhancers	Fetal Stomach	stomach
45	chr11:4092800-4094200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:4092800-4094200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:4093000-4094000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:4093000-4094000	Enhancers	Brain Angular Gyrus	brain
49	chr11:4093000-4094000	Enhancers	Brain Hippocampus Middle	brain
50	chr11:4093000-4094000	Enhancers	Duodenum Smooth Muscle	Duodenum

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