Variant report

Variant	rs1662162
Chromosome Location	chr11:4115264-4115265
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	chr11:4114893-4115634	GM12878	blood:	n/a	n/a
2	RCOR1	chr11:4115227-4116501	Hela-S3	cervix:	n/a	n/a
3	MAX	chr11:4115241-4116596	NB4	blood:	n/a	chr11:4115983-4115992
4	POLR2A	chr11:4115179-4117219	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr11:4115100-4117543	GM12892	blood:	n/a	n/a
6	YY1	chr11:4115178-4116704	SK-N-SH	brain:	n/a	chr11:4116379-4116388 chr11:4115931-4115948 chr11:4115840-4115852 chr11:4116458-4116472 chr11:4115937-4115947 chr11:4115930-4115949 chr11:4115836-4115853 chr11:4115841-4115850 chr11:4115925-4115947 chr11:4116307-4116321 chr11:4115830-4115852 chr11:4115936-4115944
7	POLR2A	chr11:4115026-4116655	GM12892	blood:	n/a	n/a
8	POLR2A	chr11:4115231-4116649	PFSK-1	brain:	n/a	n/a
9	TCF12	chr11:4115223-4116490	A549	lung:	n/a	n/a
10	POLR2A	chr11:4115223-4116336	GM12891	blood:	n/a	n/a
11	POLR2A	chr11:4115051-4117511	U87	brain:	n/a	n/a
12	RCOR1	chr11:4115055-4117422	K562	blood:	n/a	n/a
13	POLR2A	chr11:4115183-4117322	Raji	blood:	n/a	n/a
14	POLR2A	chr11:4114949-4117449	U87	brain:	n/a	n/a
15	POLR2A	chr11:4115250-4117739	IMR90	lung:	n/a	n/a
16	TBL1XR1	chr11:4115237-4116286	K562	blood:	n/a	n/a
17	POLR2A	chr11:4115151-4116313	HepG2	liver:	n/a	n/a
18	POLR2A	chr11:4114994-4116405	PANC-1	pancreas:	n/a	n/a
19	IRF1	chr11:4115172-4116266	K562	blood:	n/a	n/a
20	TEAD4	chr11:4115060-4116385	K562	blood:	n/a	n/a
21	REST	chr11:4115045-4117166	H1-neurons	neurons:	n/a	chr11:4115215-4115228
22	POLR2A	chr11:4115039-4116309	MCF10A-Er-Src	breast:	n/a	n/a
23	CREB1	chr11:4115256-4116621	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:4114998-4116722	GM12878	blood:	n/a	n/a
25	POLR2A	chr11:4115003-4116673	GM18951	blood:	n/a	n/a
26	POLR2A	chr11:4115190-4116583	K562	blood:	n/a	n/a
27	POLR2A	chr11:4115102-4116464	GM12892	blood:	n/a	n/a
28	POLR2A	chr11:4115249-4116764	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr11:4115206-4116557	K562	blood:	n/a	n/a
30	POLR2A	chr11:4115005-4117761	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr11:4115031-4117796	HepG2	liver:	n/a	n/a
32	POLR2A	chr11:4112420-4117868	K562	blood:	n/a	n/a
33	GTF2F1	chr11:4115241-4116302	Hela-S3	cervix:	n/a	n/a
34	BACH1	chr11:4115182-4116219	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr11:4114997-4116644	GM12891	blood:	n/a	n/a
36	POLR2A	chr11:4115040-4117205	K562	blood:	n/a	n/a
37	TAF1	chr11:4115253-4116522	H1-hESC	embryonic stem cell:	n/a	n/a
38	TBP	chr11:4115192-4117033	K562	blood:	n/a	n/a
39	HA-E2F1	chr11:4115199-4117048	MCF-7	breast:	n/a	chr11:4116373-4116382 chr11:4116051-4116062 chr11:4116365-4116372 chr11:4116374-4116381 chr11:4116051-4116063 chr11:4116365-4116372 chr11:4116373-4116385 chr11:4116311-4116321 chr11:4116308-4116318 chr11:4116365-4116372 chr11:4116049-4116058 chr11:4116374-4116381 chr11:4116374-4116381
40	POLR2A	chr11:4115015-4116797	K562	blood:	n/a	n/a
41	POLR2A	chr11:4114936-4118198	Hela-S3	cervix:	n/a	n/a
42	HCFC1	chr11:4114838-4117374	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr11:4115188-4116539	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr11:4114955-4116463	HepG2	liver:	n/a	n/a
45	STAT5A	chr11:4115098-4116687	GM12878	blood:	n/a	n/a
46	TFAP2C	chr11:4115256-4117106	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr11:4114997-4116816	GM12892	blood:	n/a	n/a
48	POLR2A	chr11:4115131-4116603	K562	blood:	n/a	n/a
49	POLR2A	chr11:4114998-4117877	GM12878	blood:	n/a	n/a
50	CREB1	chr11:4115216-4116655	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:4114277..4116935-chr11:4123036..4125551,3	K562	blood:
2	chr11:4109002..4112620-chr11:4113600..4116906,4	MCF-7	breast:
3	chr11:3859988..3862622-chr11:4113266..4115501,2	K562	blood:

Variant related genes	Relation type
RRM1	TF binding region
ENSG00000167325	Chromatin interaction
ENSG00000177105	Chromatin interaction
ENSG00000167323	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1036847	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1042858	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1042919	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1042927	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10500594	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10742239	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10742244	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10742245	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10742246	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10742247	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10767827	0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10767828	0.85[ASN][1000 genomes]
rs10767844	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10767849	0.85[EUR][1000 genomes]
rs10767850	0.85[EUR][1000 genomes]
rs10767851	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10767853	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10767854	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10767855	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10767857	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10767858	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10835605	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10835662	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835679	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11030841	0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs11031097	0.85[EUR][1000 genomes]
rs11031100	0.85[EUR][1000 genomes]
rs11031123	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1348310	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1474500	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561876	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1735068	0.89[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284451	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232043	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs2412342	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2412343	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2412370	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2898949	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794050	0.83[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4243967	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4492817	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4570574	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910601	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910882	0.85[ASN][1000 genomes]
rs4910883	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4910893	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910894	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910895	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs4910896	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910897	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910898	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910899	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910900	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910903	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910905	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910906	0.82[EUR][1000 genomes]
rs4910907	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910908	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910909	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910910	0.89[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910911	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910912	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56336381	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6578440	0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6578446	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6578448	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs7103860	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7104462	0.85[ASN][1000 genomes]
rs7115496	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7126014	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7358436	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7932271	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7933164	0.85[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap]
rs7938727	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7940497	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7945413	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7945532	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7946885	1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7946987	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7950384	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7951836	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9666853	0.80[EUR][1000 genomes]
rs992980	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

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	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
3	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
4	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
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1662162	RRM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4106600-4115400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:4108200-4115400	Weak transcription	Small Intestine	intestine
3	chr11:4113000-4115400	Weak transcription	Ovary	ovary
4	chr11:4113200-4115400	Weak transcription	Lung	lung
5	chr11:4113400-4115400	Weak transcription	Gastric	stomach
6	chr11:4113400-4115400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:4114800-4115400	Enhancers	Pancreas	Pancrea
8	chr11:4114800-4115400	Enhancers	Spleen	Spleen
9	chr11:4115000-4115400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:4115000-4115400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:4115000-4115400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:4115000-4115400	Flanking Active TSS	Colon Smooth Muscle	Colon
13	chr11:4115000-4115400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr11:4115000-4115400	Flanking Active TSS	GM12878-XiMat	blood
15	chr11:4115000-4115600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:4115000-4115600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr11:4115000-4115600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:4115000-4115600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr11:4115000-4115600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr11:4115000-4115600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr11:4115000-4115600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:4115000-4115600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr11:4115000-4115600	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr11:4115000-4115600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr11:4115000-4115600	Flanking Active TSS	Fetal Stomach	stomach
26	chr11:4115000-4115600	Flanking Active TSS	Dnd41	blood
27	chr11:4115000-4115600	Flanking Active TSS	Hela-S3	cervix
28	chr11:4115000-4115600	Flanking Active TSS	Osteobl	bone
29	chr11:4115000-4116600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:4115000-4116600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:4115000-4116600	Active TSS	Brain Germinal Matrix	brain
32	chr11:4115000-4116600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:4115000-4116600	Active TSS	HMEC	breast
34	chr11:4115000-4116600	Active TSS	HSMMtube	muscle
35	chr11:4115000-4117000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:4115000-4117000	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr11:4115000-4117000	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr11:4115000-4117000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr11:4115000-4117000	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr11:4115000-4117000	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr11:4115000-4117200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:4115000-4117200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr11:4115000-4117400	Active TSS	H1 Cell Line	embryonic stem cell
44	chr11:4115000-4117400	Active TSS	H9 Cell Line	embryonic stem cell
45	chr11:4115000-4117400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:4115000-4117600	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr11:4115200-4115400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:4115200-4115400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:4115200-4115400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:4115200-4115400	Enhancers	Primary neutrophils fromperipheralblood	blood

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