Variant report

Variant	rs2071027
Chromosome Location	chr4:48139752-48139753
allele	A/G
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	POLR2A	chr4:48139451-48140203	GM12891	blood:	n/a	n/a
2	POLR2A	chr4:48139666-48140134	GM12891	blood:	n/a	n/a
3	POLR2A	chr4:48139566-48140027	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:48139345-48141304	GM12892	blood:	n/a	n/a
5	POLR2A	chr4:48139749-48140119	GM12891	blood:	n/a	n/a
6	POLR2A	chr4:48139673-48140234	GM12892	blood:	n/a	n/a
7	POLR2A	chr4:48139379-48140215	GM12892	blood:	n/a	n/a
8	POLR2A	chr4:48139471-48140206	GM12878	blood:	n/a	n/a
9	POLR2A	chr4:48139684-48140135	GM12892	blood:	n/a	n/a
10	POLR2A	chr4:48137778-48141212	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48139300..48141926-chr4:48270547..48272865,2	MCF-7	breast:
2	chr4:48131478..48133698-chr4:48139197..48141386,3	K562	blood:

Variant related genes	Relation type
TXK	TF binding region
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1008277	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10805164	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10805165	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10938522	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11730441	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11733531	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11941829	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11945978	0.88[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs12502268	0.82[EUR][1000 genomes]
rs12502528	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512837	0.83[EUR][1000 genomes]
rs12649067	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13104849	0.96[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap]
rs13146998	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1466990	0.83[EUR][1000 genomes]
rs1466991	0.83[EUR][1000 genomes]
rs1466992	0.83[EUR][1000 genomes]
rs1466993	0.83[EUR][1000 genomes]
rs1466994	0.88[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1466995	0.83[EUR][1000 genomes]
rs1466996	0.83[EUR][1000 genomes]
rs1961974	0.83[EUR][1000 genomes]
rs1961975	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2089509	0.88[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2089511	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2256425	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271173	0.85[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2271174	0.83[EUR][1000 genomes]
rs34990592	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792620	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs3792621	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs3792622	0.96[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs3805179	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs3913948	0.86[EUR][1000 genomes]
rs4323077	0.83[EUR][1000 genomes]
rs4392481	0.83[EUR][1000 genomes]
rs4392482	0.82[EUR][1000 genomes]
rs4504220	0.82[EUR][1000 genomes]
rs4695339	0.83[EUR][1000 genomes]
rs4695340	0.88[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs4695342	0.83[EUR][1000 genomes]
rs4695343	0.83[EUR][1000 genomes]
rs4695344	0.88[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs4695346	0.83[EUR][1000 genomes]
rs4695347	0.83[EUR][1000 genomes]
rs4695348	0.83[EUR][1000 genomes]
rs4695349	0.83[EUR][1000 genomes]
rs4695350	0.83[EUR][1000 genomes]
rs62309327	0.83[EUR][1000 genomes]
rs6844543	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845941	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6851861	0.82[EUR][1000 genomes]
rs6858716	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7654108	0.83[EUR][1000 genomes]
rs7668350	0.82[EUR][1000 genomes]
rs7669393	0.83[EUR][1000 genomes]
rs7670351	0.83[EUR][1000 genomes]
rs7671720	0.81[EUR][1000 genomes]
rs7680519	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695902	0.83[EUR][1000 genomes]
rs7696119	0.83[EUR][1000 genomes]
rs7696271	0.83[EUR][1000 genomes]
rs885443	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs955691	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2071027	FRYL	cis	cerebellum	SCAN
rs2071027	NFXL1	cis	multi-tissue	Pritchard

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48129800-48140800	Weak transcription	Fetal Stomach	stomach
2	chr4:48129800-48157400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:48130400-48139800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:48130400-48152200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:48130400-48155400	Weak transcription	Psoas Muscle	Psoas
6	chr4:48130400-48156200	Weak transcription	Adipose Nuclei	Adipose
7	chr4:48130400-48156800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:48130400-48157600	Weak transcription	Colonic Mucosa	Colon
9	chr4:48130600-48142800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:48130600-48146000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:48131800-48141400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:48131800-48142000	Weak transcription	NHLF	lung
13	chr4:48132000-48141400	Weak transcription	HUVEC	blood vessel
14	chr4:48132000-48141600	Weak transcription	NHDF-Ad	bronchial
15	chr4:48132000-48157000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:48132000-48157200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:48132200-48139800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:48132200-48141800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:48132400-48142000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:48132600-48140200	Weak transcription	Right Ventricle	heart
21	chr4:48132600-48141000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:48133000-48141800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:48133000-48151400	Weak transcription	HSMMtube	muscle
24	chr4:48133000-48153000	Weak transcription	Placenta	Placenta
25	chr4:48133200-48140400	Weak transcription	Left Ventricle	heart
26	chr4:48133200-48141000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:48133200-48141800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:48134600-48140600	Weak transcription	Fetal Kidney	kidney
29	chr4:48134800-48141400	Weak transcription	Fetal Brain Male	brain
30	chr4:48135400-48140400	Strong transcription	GM12878-XiMat	blood
31	chr4:48135400-48142200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr4:48135600-48142800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:48136000-48140400	Weak transcription	Small Intestine	intestine
34	chr4:48136000-48140600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:48136000-48141000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:48136400-48139800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr4:48136400-48139800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:48136400-48141200	Strong transcription	K562	blood
39	chr4:48136600-48139800	Enhancers	Primary T cells fromperipheralblood	blood
40	chr4:48136600-48139800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:48136800-48139800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:48136800-48140600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:48137000-48139800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr4:48137000-48141200	Strong transcription	Liver	Liver
45	chr4:48137000-48141400	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr4:48137400-48140800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr4:48137600-48139800	Genic enhancers	Fetal Thymus	thymus
48	chr4:48137600-48139800	Strong transcription	Spleen	Spleen
49	chr4:48137600-48141200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:48137800-48139800	Strong transcription	Lung	lung

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