Variant report

Variant	rs10838406
Chromosome Location	chr11:5617896-5617897
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	ELF1	chr11:5617724-5618040	A549	lung:	n/a	n/a
2	CTCF	chr11:5617780-5617930	HCPEpiC	choroid plexus:	n/a	n/a
3	CCNT2	chr11:5617793-5618459	K562	blood:	n/a	chr11:5617839-5617848
4	POLR2A	chr11:5617785-5618079	A549	lung:	n/a	n/a
5	POLR2A	chr11:5617778-5618325	PANC-1	pancreas:	n/a	n/a
6	SIN3AK20	chr11:5617808-5618291	A549	lung:	n/a	n/a
7	CTCF	chr11:5617820-5617970	AG04449	skin:	n/a	n/a
8	HMGN3	chr11:5617106-5618190	K562	blood:	n/a	n/a
9	POLR2A	chr11:5617801-5618205	K562	blood:	n/a	n/a
10	TEAD4	chr11:5617663-5618546	K562	blood:	n/a	n/a
11	MAX	chr11:5617122-5618599	A549	lung:	n/a	n/a
12	SPI1	chr11:5617783-5618033	GM12891	blood:	n/a	n/a
13	SIN3A	chr11:5617804-5618474	H1-hESC	embryonic stem cell:	n/a	n/a
14	RCOR1	chr11:5617079-5618584	K562	blood:	n/a	n/a
15	ZBTB7A	chr11:5617770-5618062	K562	blood:	n/a	n/a
16	POLR2A	chr11:5617777-5618067	HCT-116	colon:	n/a	n/a
17	CEBPB	chr11:5617808-5618295	K562	blood:	n/a	n/a
18	HCFC1	chr11:5617794-5618143	K562	blood:	n/a	n/a
19	MAX	chr11:5617763-5618139	K562	blood:	n/a	n/a
20	ZNF274	chr11:5617827-5618463	K562	blood:	n/a	n/a
21	SIN3AK20	chr11:5617768-5618463	PANC-1	pancreas:	n/a	n/a
22	TBL1XR1	chr11:5617771-5618478	K562	blood:	n/a	n/a
23	POLR2A	chr11:5617881-5618046	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr11:5617787-5618082	Gliobla	brain:	n/a	n/a
25	POLR2A	chr11:5617806-5618031	A549	lung:	n/a	n/a
26	ETS1	chr11:5617777-5618211	K562	blood:	n/a	chr11:5617815-5617828
27	POLR2A	chr11:5617781-5618343	K562	blood:	n/a	n/a
28	EGR1	chr11:5617768-5618257	K562	blood:	n/a	chr11:5617816-5617825
29	STAT5A	chr11:5617772-5618351	K562	blood:	n/a	n/a
30	TAF1	chr11:5617776-5618163	K562	blood:	n/a	n/a
31	POLR2A	chr11:5617774-5618200	K562	blood:	n/a	n/a
32	REST	chr11:5617800-5618099	K562	blood:	n/a	n/a
33	SPI1	chr11:5617786-5617996	K562	blood:	n/a	n/a
34	ATF1	chr11:5617834-5618374	K562	blood:	n/a	n/a
35	GATA2	chr11:5617717-5618502	K562	blood:	n/a	chr11:5618210-5618219 chr11:5618212-5618219
36	GATA2	chr11:5617775-5618269	K562	blood:	n/a	chr11:5618210-5618219 chr11:5618212-5618219
37	SRF	chr11:5617785-5618147	K562	blood:	n/a	n/a
38	POLR2A	chr11:5617113-5618552	PANC-1	pancreas:	n/a	n/a
39	TAF1	chr11:5617784-5618368	A549	lung:	n/a	n/a
40	SPI1	chr11:5617798-5618010	K562	blood:	n/a	n/a
41	GATA1	chr11:5617848-5618510	PBDE	blood:	n/a	chr11:5618210-5618219 chr11:5618212-5618219
42	TRIM28	chr11:5617776-5618437	K562	blood:	n/a	n/a
43	HDAC2	chr11:5617786-5618461	K562	blood:	n/a	chr11:5618249-5618263 chr11:5618248-5618262 chr11:5618253-5618267
44	TAF1	chr11:5617770-5618025	H1-hESC	embryonic stem cell:	n/a	n/a
45	GABPA	chr11:5617756-5618171	K562	blood:	n/a	n/a
46	POLR2A	chr11:5617798-5618053	A549	lung:	n/a	n/a
47	NR2F2	chr11:5617689-5618538	K562	blood:	n/a	n/a
48	ELF1	chr11:5617723-5618027	A549	lung:	n/a	n/a
49	EP300	chr11:5617808-5618355	K562	blood:	n/a	chr11:5618252-5618266
50	TCF7L2	chr11:5617174-5618113	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:5522829..5527225-chr11:5617678..5621647,5	K562	blood:

Variant related genes	Relation type
TRIM6-TRIM34	TF binding region
TRIM6	TF binding region
ENSG00000196565	Chromatin interaction
ENSG00000213931	Chromatin interaction
ENSG00000167355	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs6578665	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7106584	0.86[ASW][hapmap]
rs7121553	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
2	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	nsv896943	chr11:5583188-5619008	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv896944	chr11:5588174-5625603	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv896945	chr11:5598864-5625603	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1054035	chr11:5604437-5620417	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv2760210	chr11:5604437-5620429	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1048455	chr11:5609783-5655393	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
13	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10838406	UBQLNL	cis	lymphoblastoid	seeQTL
rs10838406	FAM75D1	trans	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5617000-5618000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:5617000-5618000	Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr11:5617000-5618000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:5617000-5618000	Active TSS	Adipose Nuclei	Adipose
5	chr11:5617000-5618200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr11:5617000-5618200	Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr11:5617000-5618400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr11:5617000-5618800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr11:5617000-5619000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr11:5617000-5619200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr11:5617000-5619400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr11:5617200-5618000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:5617200-5618000	Active TSS	Brain Hippocampus Middle	brain
14	chr11:5617200-5618000	Active TSS	Placenta	Placenta
15	chr11:5617200-5618200	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr11:5617200-5618200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:5617200-5618200	Active TSS	Duodenum Mucosa	Duodenum
18	chr11:5617200-5618200	Active TSS	Esophagus	oesophagus
19	chr11:5617200-5618200	Active TSS	Fetal Brain Female	brain
20	chr11:5617200-5618200	Active TSS	Rectal Smooth Muscle	rectum
21	chr11:5617200-5618200	Active TSS	Osteobl	bone
22	chr11:5617200-5618400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:5617200-5618400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:5617200-5618400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:5617200-5618400	Active TSS	Aorta	Aorta
26	chr11:5617200-5618400	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr11:5617200-5618400	Active TSS	Fetal Intestine Large	intestine
28	chr11:5617200-5618400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr11:5617200-5618400	Active TSS	Psoas Muscle	Psoas
30	chr11:5617200-5618400	Active TSS	Right Atrium	heart
31	chr11:5617200-5618400	Active TSS	Right Ventricle	heart
32	chr11:5617200-5618600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:5617200-5618600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:5617200-5618600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr11:5617200-5618600	Active TSS	Monocytes-CD14+_RO01746	blood
36	chr11:5617200-5618800	Active TSS	H1 Cell Line	embryonic stem cell
37	chr11:5617200-5618800	Active TSS	Stomach Smooth Muscle	stomach
38	chr11:5617200-5619000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr11:5617200-5619400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr11:5617200-5619800	Active TSS	A549	lung
41	chr11:5617400-5618000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:5617400-5618000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr11:5617400-5618000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:5617400-5618000	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr11:5617400-5618000	Active TSS	Fetal Kidney	kidney
46	chr11:5617400-5618000	Active TSS	Pancreas	Pancrea
47	chr11:5617400-5618000	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr11:5617400-5618000	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr11:5617400-5618000	Active TSS	Dnd41	blood
50	chr11:5617400-5618000	Active TSS	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links