Variant report

Variant	rs752949
Chromosome Location	chr11:35327748-35327749
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	chr11:35327224-35327764	SK-N-SH_RA	brain:	n/a	chr11:35327602-35327616 chr11:35327513-35327532
2	SMC3	chr11:35326849-35327935	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr11:35327288-35327773	MCF-7	breast:	n/a	chr11:35327510-35327531 chr11:35327515-35327533 chr11:35327516-35327532
4	RAD21	chr11:35327084-35327877	SK-N-SH	brain:	n/a	chr11:35327602-35327616 chr11:35327513-35327532
5	RAD21	chr11:35327219-35327767	A549	lung:	n/a	chr11:35327602-35327616 chr11:35327513-35327532
6	CTCF	chr11:35327700-35327850	NHLF	lung:	n/a	n/a
7	RAD21	chr11:35327248-35327777	H1-hESC	embryonic stem cell:	n/a	chr11:35327602-35327616 chr11:35327513-35327532
8	RAD21	chr11:35327286-35327808	ECC-1	luminal epithelium:	n/a	chr11:35327602-35327616 chr11:35327513-35327532
9	MAFK	chr11:35327311-35327761	Hela-S3	cervix:	n/a	chr11:35327531-35327547 chr11:35327532-35327546 chr11:35327538-35327549 chr11:35327537-35327551 chr11:35327529-35327549 chr11:35327533-35327543 chr11:35327536-35327545 chr11:35327534-35327549
10	MAFF	chr11:35327306-35327758	HepG2	liver:	n/a	chr11:35327533-35327551 chr11:35327532-35327546
11	MAFK	chr11:35326999-35327948	GM12878	blood:	n/a	chr11:35327531-35327547 chr11:35327532-35327546 chr11:35327538-35327549 chr11:35327537-35327551 chr11:35327529-35327549 chr11:35327533-35327543 chr11:35327536-35327545 chr11:35327534-35327549
12	MAFK	chr11:35327286-35327784	K562	blood:	n/a	chr11:35327531-35327547 chr11:35327532-35327546 chr11:35327538-35327549 chr11:35327537-35327551 chr11:35327529-35327549 chr11:35327533-35327543 chr11:35327536-35327545 chr11:35327534-35327549
13	RAD21	chr11:35327189-35327782	HCT-116	colon:	n/a	chr11:35327602-35327616 chr11:35327513-35327532
14	CTCF	chr11:35327205-35327795	HCT-116	colon:	n/a	chr11:35327510-35327531 chr11:35327515-35327533 chr11:35327516-35327532
15	YY1	chr11:35327329-35327820	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr11:35327215-35327819	MCF-7	breast:	n/a	chr11:35327602-35327616 chr11:35327513-35327532
17	MAFK	chr11:35327333-35327852	H1-hESC	embryonic stem cell:	n/a	chr11:35327531-35327547 chr11:35327532-35327546 chr11:35327538-35327549 chr11:35327537-35327551 chr11:35327529-35327549 chr11:35327533-35327543 chr11:35327536-35327545 chr11:35327534-35327549
18	CTCF	chr11:35327379-35327786	GM19240	blood:	n/a	chr11:35327510-35327531 chr11:35327515-35327533 chr11:35327516-35327532
19	CTCF	chr11:35327033-35327886	SK-N-SH	brain:	n/a	chr11:35327510-35327531 chr11:35327515-35327533 chr11:35327516-35327532
20	TCF7L2	chr11:35327307-35327750	Hela-S3	cervix:	n/a	chr11:35327535-35327544
21	MAFF	chr11:35327304-35327755	K562	blood:	n/a	chr11:35327533-35327551 chr11:35327532-35327546
22	MAFK	chr11:35327146-35327905	IMR90	lung:	n/a	chr11:35327531-35327547 chr11:35327532-35327546 chr11:35327538-35327549 chr11:35327537-35327551 chr11:35327529-35327549 chr11:35327533-35327543 chr11:35327536-35327545 chr11:35327534-35327549
23	RAD21	chr11:35327106-35327760	MCF-7	breast:	n/a	chr11:35327602-35327616 chr11:35327513-35327532
24	RAD21	chr11:35327242-35327831	HCT-116	colon:	n/a	chr11:35327602-35327616 chr11:35327513-35327532
25	CTCF	chr11:35327276-35327796	MCF-7	breast:	n/a	chr11:35327510-35327531 chr11:35327515-35327533 chr11:35327516-35327532

No.	Distal block	Cell Line	Cell type
1	chr11:35316164..35320832-chr11:35323901..35327904,6	MCF-7	breast:
2	chr11:35294659..35299259-chr11:35323739..35329418,10	MCF-7	breast:
3	chr11:35325082..35329028-chr11:35338650..35340551,3	MCF-7	breast:
4	chr11:35327322..35328895-chr11:35375252..35377771,2	MCF-7	breast:
5	chr11:35282903..35283518-chr11:35327015..35328007,3	MCF-7	breast:
6	chr11:35325412..35330750-chr11:35411649..35414159,5	MCF-7	breast:
7	chr11:35325471..35328883-chr11:35329361..35332564,3	MCF-7	breast:

Variant related genes	Relation type
SLC1A2	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1042113	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10444271	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10488816	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10488817	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10488818	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10836366	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10836368	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11033050	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11033053	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11033054	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11033055	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11033056	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11033057	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11033058	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11033060	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11033063	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11033064	0.94[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11033071	0.84[CHB][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap]
rs12146523	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12418812	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12574069	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs12576364	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12576375	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16927292	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236272	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3794087	0.92[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3794088	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3794093	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794094	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794097	0.85[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3829266	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3847612	0.84[CHB][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap]
rs3847613	0.84[CHB][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs3891872	0.90[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3895234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911898	0.84[JPT][hapmap]
rs4083481	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs41352148	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41427147	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs41525047	0.89[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4756207	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4756211	0.84[CHB][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap]
rs56043665	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56140126	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56402269	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61880962	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882290	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61882291	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61882292	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61882293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7111043	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111055	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7111179	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7129693	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72638196	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72638197	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7927975	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7940391	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv832120	chr11:35277410-35490304	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2758264	chr11:35319320-35480522	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2759819	chr11:35319320-35480522	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs752949	C11orf41	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35299800-35328600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr11:35302600-35329000	Weak transcription	Brain Angular Gyrus	brain
3	chr11:35314200-35329200	Weak transcription	Fetal Brain Male	brain
4	chr11:35324000-35327800	Enhancers	NHLF	lung
5	chr11:35324000-35336200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr11:35324400-35343200	Weak transcription	Gastric	stomach
7	chr11:35325200-35327800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:35325200-35327800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:35325200-35328600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr11:35325200-35339000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr11:35325400-35327800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:35325400-35327800	Strong transcription	Fetal Brain Female	brain
13	chr11:35325600-35327800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr11:35325600-35327800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:35325600-35327800	Enhancers	Placenta	Placenta
16	chr11:35325600-35327800	Enhancers	Stomach Smooth Muscle	stomach
17	chr11:35325600-35339200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:35325800-35327800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:35325800-35327800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr11:35325800-35327800	Strong transcription	Brain Germinal Matrix	brain
21	chr11:35325800-35327800	Enhancers	Spleen	Spleen
22	chr11:35325800-35327800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr11:35326000-35327800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr11:35326400-35327800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr11:35326400-35327800	ZNF genes & repeats	Liver	Liver
26	chr11:35326400-35327800	Enhancers	Brain Anterior Caudate	brain
27	chr11:35326600-35327800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:35326600-35327800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:35326800-35327800	Enhancers	Primary hematopoietic stem cells	blood
30	chr11:35327000-35327800	Enhancers	Primary B cells from peripheral blood	blood
31	chr11:35327000-35327800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:35327000-35327800	Enhancers	Brain Cingulate Gyrus	brain
33	chr11:35327000-35327800	Enhancers	Fetal Stomach	stomach
34	chr11:35327000-35333400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:35327000-35343400	Weak transcription	Fetal Lung	lung
36	chr11:35327200-35327800	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr11:35327200-35327800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr11:35327200-35327800	Enhancers	Brain Hippocampus Middle	brain
39	chr11:35327200-35327800	Enhancers	Duodenum Mucosa	Duodenum
40	chr11:35327200-35327800	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr11:35327200-35327800	Enhancers	K562	blood
42	chr11:35327200-35340600	Weak transcription	Brain Substantia Nigra	brain
43	chr11:35327400-35327800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr11:35327400-35327800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:35327400-35327800	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr11:35327400-35327800	Enhancers	Left Ventricle	heart
47	chr11:35327400-35327800	Genic enhancers	Pancreas	Pancrea
48	chr11:35327400-35327800	Enhancers	GM12878-XiMat	blood
49	chr11:35327400-35328400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr11:35327400-35328600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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