Variant report

Variant	rs11903212
Chromosome Location	chr2:58423312-58423313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10167028	0.91[CEU][hapmap]
rs10184957	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10187411	0.80[MKK][hapmap];0.86[YRI][hapmap]
rs10198382	0.83[CEU][hapmap];0.94[GIH][hapmap]
rs10203887	0.91[CEU][hapmap]
rs10518852	0.80[MKK][hapmap]
rs12616896	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12624152	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713376	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12713378	0.94[JPT][hapmap]
rs12988249	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13001078	0.91[CEU][hapmap]
rs13006005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13023405	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13032851	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13033987	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs13382369	0.80[MKK][hapmap]
rs13384786	0.91[CEU][hapmap];0.94[GIH][hapmap]
rs13386998	0.83[CEU][hapmap]
rs13397947	0.83[AFR][1000 genomes]
rs13410228	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13422760	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13424099	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs13431271	0.80[MKK][hapmap]
rs1371213	0.81[YRI][hapmap]
rs1404457	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1404459	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1404460	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17183100	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2165100	0.80[MKK][hapmap]
rs2312486	0.86[YRI][hapmap]
rs34335951	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34556232	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35341336	0.81[EUR][1000 genomes]
rs35773188	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35925771	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755296	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771220	0.83[CEU][hapmap]
rs3771222	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55809167	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57267169	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61746304	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6709533	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6714952	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6740373	0.87[AFR][1000 genomes]
rs6740836	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs6742445	0.96[AFR][1000 genomes]
rs6752935	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72948876	0.94[AFR][1000 genomes]
rs7340170	0.95[YRI][hapmap];0.92[AFR][1000 genomes]
rs7558066	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7561771	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7569731	0.86[YRI][hapmap]
rs7590976	0.84[ASW][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs7597069	0.88[AFR][1000 genomes]
rs9309303	0.90[YRI][hapmap]
rs9973679	0.94[JPT][hapmap]
rs9973912	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv1804150	chr2:58418501-58431168	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11903212	FANCL	cis	lymphoblastoid	seeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:58385200-58424600	Weak transcription	Ovary	ovary
4	chr2:58388800-58437400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:58389600-58431000	Weak transcription	HUVEC	blood vessel
6	chr2:58391000-58467000	Weak transcription	HMEC	breast
7	chr2:58396400-58438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:58396400-58438000	Weak transcription	Pancreas	Pancrea
9	chr2:58397800-58442600	Weak transcription	Brain Anterior Caudate	brain
10	chr2:58398000-58437800	Weak transcription	Primary B cells from cord blood	blood
11	chr2:58399400-58437400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:58399800-58426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:58400400-58437800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:58403000-58439400	Weak transcription	HSMM	muscle
15	chr2:58403600-58434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:58403600-58437200	Weak transcription	Fetal Brain Female	brain
17	chr2:58407400-58424000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:58407600-58425000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:58410400-58425200	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:58411600-58437400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:58413800-58425000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:58413800-58438000	Weak transcription	Thymus	Thymus
23	chr2:58414000-58437600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:58414000-58461400	Weak transcription	NHEK	skin
25	chr2:58414200-58429800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:58414200-58435800	Weak transcription	Fetal Intestine Small	intestine
27	chr2:58414400-58438000	Weak transcription	Esophagus	oesophagus
28	chr2:58414600-58425000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:58414600-58437400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:58414600-58437400	Weak transcription	Brain Germinal Matrix	brain
31	chr2:58415000-58430400	Weak transcription	NHDF-Ad	bronchial
32	chr2:58415000-58437600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:58415400-58434000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr2:58415800-58437400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:58416000-58437400	Weak transcription	Fetal Kidney	kidney
36	chr2:58416200-58437400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:58416200-58454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:58416400-58424600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:58416400-58424600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:58416400-58425200	Weak transcription	Fetal Intestine Large	intestine
41	chr2:58416400-58433400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:58416400-58434000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:58416400-58437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:58416400-58438000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr2:58416600-58425000	Weak transcription	Fetal Lung	lung
46	chr2:58416600-58467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:58416800-58424600	Weak transcription	HepG2	liver
48	chr2:58417800-58439200	Weak transcription	Fetal Brain Male	brain
49	chr2:58420000-58432400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:58421200-58425000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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