Variant report

Variant	rs16927292
Chromosome Location	chr11:35327041-35327042
allele	A/C
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	SMC3	chr11:35326849-35327935	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr11:35325489-35327231	PFSK-1	brain:	n/a	n/a
3	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
4	CTCF	chr11:35327033-35327886	SK-N-SH	brain:	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	chr11:34947799..34948300-chr11:35326589..35327576,2	K562	blood:
4	chr11:35325082..35329028-chr11:35338650..35340551,3	MCF-7	breast:
5	chr11:35325349..35327206-chr11:35381816..35384283,2	MCF-7	breast:
6	chr11:35282903..35283518-chr11:35327015..35328007,3	MCF-7	breast:
7	chr11:35325412..35330750-chr11:35411649..35414159,5	MCF-7	breast:
8	chr11:35316339..35320306-chr11:35324557..35327417,4	MCF-7	breast:
9	chr11:35325471..35328883-chr11:35329361..35332564,3	MCF-7	breast:

Variant related genes	Relation type
SLC1A2	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1042113	0.84[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10444271	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10488816	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10488817	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10488818	0.90[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10836366	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10836368	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11033050	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11033053	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11033054	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11033055	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11033056	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11033057	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11033058	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11033060	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11033063	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11033064	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11033071	0.92[CHB][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs11033080	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs12146523	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12418812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574069	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs12576364	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12576375	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2236272	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2273687	0.81[AMR][1000 genomes]
rs3794087	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3794088	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3794093	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3794094	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3794097	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812778	0.84[MKK][hapmap];1.00[YRI][hapmap]
rs3829266	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3847612	0.92[CHB][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes]
rs3847613	0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs3847620	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs3891872	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3895234	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3911898	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4083481	0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs41352148	0.90[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41427147	0.90[CEU][hapmap];0.92[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs41525047	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756207	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756210	0.81[AMR][1000 genomes]
rs4756211	0.92[CHB][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs4756219	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs4756220	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs4756221	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs55709010	0.81[AMR][1000 genomes]
rs55834429	0.81[AMR][1000 genomes]
rs56043665	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56140126	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56402269	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61880962	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61882290	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61882291	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61882292	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61882293	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6484785	0.83[CHB][hapmap]
rs7111043	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7111055	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7111179	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7114383	0.83[CHB][hapmap]
rs7129693	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72638196	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72638197	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs752949	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]
rs7927975	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7934047	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs7940391	0.92[AMR][1000 genomes];0.91[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
rs16927292	C11orf41	cis	parietal	SCAN

Chromatin state (count:80 , 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	chr11:35317600-35327600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:35322600-35327400	Enhancers	Adipose Nuclei	Adipose
6	chr11:35324000-35327600	Enhancers	NHDF-Ad	bronchial
7	chr11:35324000-35327800	Enhancers	NHLF	lung
8	chr11:35324000-35336200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr11:35324200-35327600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr11:35324200-35327600	Enhancers	Osteobl	bone
11	chr11:35324400-35327200	Weak transcription	Esophagus	oesophagus
12	chr11:35324400-35327200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:35324400-35343200	Weak transcription	Gastric	stomach
14	chr11:35324600-35327200	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:35324800-35327600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:35325200-35327800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:35325200-35327800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:35325200-35328600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:35325200-35339000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:35325400-35327400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr11:35325400-35327400	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr11:35325400-35327800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:35325400-35327800	Strong transcription	Fetal Brain Female	brain
24	chr11:35325600-35327200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr11:35325600-35327200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:35325600-35327400	Enhancers	Pancreas	Pancrea
27	chr11:35325600-35327800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr11:35325600-35327800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:35325600-35327800	Enhancers	Placenta	Placenta
30	chr11:35325600-35327800	Enhancers	Stomach Smooth Muscle	stomach
31	chr11:35325600-35339200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:35325800-35327200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr11:35325800-35327400	Enhancers	Colon Smooth Muscle	Colon
34	chr11:35325800-35327400	Enhancers	NH-A	brain
35	chr11:35325800-35327600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:35325800-35327800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:35325800-35327800	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr11:35325800-35327800	Strong transcription	Brain Germinal Matrix	brain
39	chr11:35325800-35327800	Enhancers	Spleen	Spleen
40	chr11:35325800-35327800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr11:35326000-35327200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr11:35326000-35327200	Enhancers	Brain Substantia Nigra	brain
43	chr11:35326000-35327400	Enhancers	Primary T cells from cord blood	blood
44	chr11:35326000-35327600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:35326000-35327800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr11:35326200-35327200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr11:35326200-35327200	Weak transcription	Right Atrium	heart
48	chr11:35326200-35327200	Weak transcription	A549	lung
49	chr11:35326200-35327400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:35326200-35327400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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