Variant report

Variant	rs1391221
Chromosome Location	chr11:85955279-85955280
allele	C/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	NFIC	chr11:85955169-85956481	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:85954999-85957069	K562	blood:	n/a	n/a
3	POLR2A	chr11:85955099-85957048	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr11:85955161-85956665	A549	lung:	n/a	n/a
5	NFIC	chr11:85955236-85956658	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:85955169-85958241	GM12878	blood:	n/a	n/a
7	MAX	chr11:85955109-85957035	HCT-116	colon:	n/a	chr11:85955874-85955884
8	BHLHE40	chr11:85955215-85957057	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:85955115-85956608	U87	brain:	n/a	n/a
10	CHD1	chr11:85955099-85957902	IMR90	lung:	n/a	n/a
11	RELA	chr11:85955249-85957148	GM15510	blood:	n/a	n/a
12	CHD2	chr11:85955260-85956584	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr11:85955192-85956707	HCT-116	colon:	n/a	n/a
14	POLR2A	chr11:85955258-85956419	HepG2	liver:	n/a	n/a
15	KAP1	chr11:85955081-85956697	U2OS	brain:	n/a	n/a
16	NFIC	chr11:85955214-85957047	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:85955263-85957049	GM12892	blood:	n/a	n/a
18	POLR2A	chr11:85954474-85957337	GM12891	blood:	n/a	n/a
19	JUND	chr11:85954403-85956517	K562	blood:	n/a	n/a
20	POLR2A	chr11:85954820-85957212	GM12878	blood:	n/a	n/a
21	POLR2A	chr11:85955002-85957058	GM18951	blood:	n/a	n/a
22	FOSL2	chr11:85955104-85956465	A549	lung:	n/a	n/a
23	POLR2A	chr11:85954919-85957181	Hela-S3	cervix:	n/a	n/a
24	SREBP1	chr11:85954186-85957169	GM12878	blood:	n/a	n/a
25	MAFK	chr11:85955210-85956375	Hela-S3	cervix:	n/a	n/a
26	SIX5	chr11:85955172-85956558	A549	lung:	n/a	chr11:85956484-85956500
27	TBL1XR1	chr11:85955179-85957119	GM12878	blood:	n/a	n/a
28	RCOR1	chr11:85955072-85956815	K562	blood:	n/a	n/a
29	CHD2	chr11:85955070-85956631	H1-hESC	embryonic stem cell:	n/a	n/a
30	SETDB1	chr11:85955048-85955791	U2OS	brain:	n/a	chr11:85955555-85955564
31	POLR2A	chr11:85954922-85957103	GM12892	blood:	n/a	n/a
32	POLR2A	chr11:85955077-85956920	MCF-7	breast:	n/a	n/a
33	POLR2A	chr11:85955200-85956556	HUVEC	blood vessel:	n/a	n/a
34	MYBL2	chr11:85955117-85956536	HepG2	liver:	n/a	n/a
35	REST	chr11:85955050-85956596	A549	lung:	n/a	chr11:85955687-85955696 chr11:85956464-85956474 chr11:85955687-85955694 chr11:85956471-85956484
36	STAT5A	chr11:85955124-85956527	GM12878	blood:	n/a	chr11:85956029-85956041 chr11:85956041-85956049 chr11:85956477-85956489 chr11:85955509-85955532
37	RUNX3	chr11:85955175-85956817	GM12878	blood:	n/a	n/a
38	ARID3A	chr11:85954407-85956646	K562	blood:	n/a	chr11:85956002-85956010
39	MAX	chr11:85955246-85956861	ECC-1	luminal epithelium:	n/a	chr11:85955874-85955884
40	CEBPB	chr11:85955135-85956452	GM12878	blood:	n/a	n/a
41	POLR2A	chr11:85955150-85957214	GM18505	blood:	n/a	n/a
42	CHD2	chr11:85955241-85957178	GM12878	blood:	n/a	n/a
43	IRF1	chr11:85954339-85956723	K562	blood:	n/a	chr11:85956519-85956536 chr11:85956226-85956240
44	POLR2A	chr11:85955150-85956631	PANC-1	pancreas:	n/a	n/a
45	CBX3	chr11:85955256-85956725	K562	blood:	n/a	chr11:85955364-85955375
46	POLR2A	chr11:85955244-85957239	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr11:85955188-85957297	GM12878	blood:	n/a	n/a
48	MYC	chr11:85954548-85956764	K562	blood:	n/a	chr11:85955874-85955884
49	BRCA1	chr11:85955082-85956392	Hela-S3	cervix:	n/a	chr11:85955370-85955377
50	BHLHE40	chr11:85955266-85956598	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:85778609..85781292-chr11:85954393..85956232,2	K562	blood:
2	chr11:85775017..85777690-chr11:85953768..85955485,2	K562	blood:
3	chr11:85871686..85873473-chr11:85953832..85955582,2	K562	blood:
4	chr11:76493928..76495285-chr11:85955090..85956457,46	Hela-S3	cervix:
5	chr11:85564358..85567668-chr11:85954757..85957283,3	MCF-7	breast:
6	chr11:85780488..85782711-chr11:85954373..85957163,3	MCF-7	breast:
7	chr11:85954509..85956884-chr11:86013356..86015049,2	K562	blood:
8	chr11:85778910..85781849-chr11:85954546..85957728,3	K562	blood:
9	chr11:85954518..85956806-chr11:85983872..85987966,3	MCF-7	breast:

Variant related genes	Relation type
EED	TF binding region
ENSG00000149196	Chromatin interaction
ENSG00000074266	Chromatin interaction
ENSG00000215504	Chromatin interaction
ENSG00000255100	Chromatin interaction
ENSG00000073921	Chromatin interaction
ENSG00000150676	Chromatin interaction
ENSG00000182704	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10792840	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898450	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898454	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10898455	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10898456	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11234582	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs11234583	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11234585	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11234586	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11234587	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11234591	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11234592	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11234595	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1215001	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12225782	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12226796	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12282663	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12574118	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12577739	0.90[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12800606	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1376947	0.87[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs19039	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2847470	0.80[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.94[YRI][hapmap]
rs291215	0.92[CHB][hapmap]
rs291216	0.80[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap]
rs291220	0.80[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs291221	0.80[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.94[YRI][hapmap]
rs291225	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs291227	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291228	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291230	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291231	0.86[EUR][1000 genomes]
rs291232	0.86[EUR][1000 genomes]
rs291233	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291234	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291235	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs291236	0.84[EUR][1000 genomes]
rs291237	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs291238	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs291242	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs291247	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs291251	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34095340	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34972740	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3923738	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4547120	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944562	0.98[EUR][1000 genomes]
rs7106569	0.80[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1391221	EED	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85954200-85955400	Flanking Active TSS	GM12878-XiMat	blood
2	chr11:85954400-85955400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
3	chr11:85954400-85955400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:85954400-85955400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr11:85954600-85955400	Flanking Active TSS	Dnd41	blood
6	chr11:85954600-85955600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:85954600-85955600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:85954800-85955400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:85954800-85955400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr11:85954800-85955400	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr11:85954800-85955400	Flanking Active TSS	Fetal Heart	heart
12	chr11:85954800-85955400	Flanking Active TSS	Hela-S3	cervix
13	chr11:85954800-85957000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:85954800-85957600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:85955000-85955400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr11:85955000-85955400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr11:85955000-85955400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr11:85955000-85955400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr11:85955000-85955400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr11:85955000-85955400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:85955000-85955400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr11:85955000-85955400	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr11:85955000-85955400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr11:85955000-85955400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr11:85955000-85955400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:85955000-85955400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr11:85955000-85955400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:85955000-85955400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:85955000-85955400	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr11:85955000-85955400	Flanking Active TSS	Liver	Liver
31	chr11:85955000-85955400	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr11:85955000-85955400	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr11:85955000-85955400	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr11:85955000-85955400	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr11:85955000-85955400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr11:85955000-85955400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:85955000-85955400	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr11:85955000-85955400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr11:85955000-85955400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr11:85955000-85955400	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr11:85955000-85955400	Flanking Active TSS	Fetal Lung	lung
42	chr11:85955000-85955400	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr11:85955000-85955400	Flanking Active TSS	Fetal Stomach	stomach
44	chr11:85955000-85955400	Flanking Active TSS	Fetal Thymus	thymus
45	chr11:85955000-85955400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr11:85955000-85955400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr11:85955000-85955400	Active TSS	Right Atrium	heart
48	chr11:85955000-85955400	Flanking Active TSS	Stomach Mucosa	stomach
49	chr11:85955000-85955400	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr11:85955000-85955400	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links