Variant report

Variant	rs3809096
Chromosome Location	chr11:18433840-18433841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr11:18433633-18434011	A549	lung:	n/a	n/a
2	E2F6	chr11:18433654-18434108	A549	lung:	n/a	chr11:18433801-18433810
3	MAX	chr11:18433686-18434039	HUVEC	blood vessel:	n/a	n/a
4	E2F6	chr11:18433520-18434234	A549	lung:	n/a	chr11:18433801-18433810
5	POLR2A	chr11:18433784-18433987	MCF-7	breast:	n/a	n/a
6	MAX	chr11:18433633-18434174	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:18433591-18434097	GM15510	blood:	n/a	n/a
8	MAX	chr11:18433662-18434085	SK-N-SH	brain:	n/a	n/a
9	JUND	chr11:18433752-18433899	H1-hESC	embryonic stem cell:	n/a	n/a
10	USF2	chr11:18433733-18433935	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr11:18433707-18434096	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr11:18433556-18434172	A549	lung:	n/a	n/a
13	POLR2A	chr11:18433682-18433991	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr11:18433586-18434098	GM18951	blood:	n/a	n/a
15	MAX	chr11:18433617-18434188	SK-N-SH	brain:	n/a	n/a
16	CREB1	chr11:18433539-18434126	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr11:18433666-18434186	Gliobla	brain:	n/a	n/a
18	TBP	chr11:18433678-18434034	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr11:18433646-18434035	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr11:18433754-18434054	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3A	chr11:18433765-18434009	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr11:18433708-18434043	A549	lung:	n/a	n/a
23	POLR2A	chr11:18433775-18433987	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr11:18433675-18434157	H1-hESC	embryonic stem cell:	n/a	n/a
25	CREB1	chr11:18433592-18434135	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr11:18433639-18434122	HEK293	kidney:	n/a	n/a
27	POLR2A	chr11:18433567-18434204	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr11:18433502-18434227	A549	lung:	n/a	n/a
29	GTF2F1	chr11:18433720-18433968	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr11:18433661-18434064	MCF-7	breast:	n/a	n/a
31	POLR2A	chr11:18433480-18434250	SK-N-MC	brain:	n/a	n/a
32	MAX	chr11:18433626-18434214	H1-hESC	embryonic stem cell:	n/a	n/a
33	EGR1	chr11:18433647-18433849	K562	blood:	n/a	n/a
34	CHD2	chr11:18433576-18433954	H1-hESC	embryonic stem cell:	n/a	n/a
35	E2F6	chr11:18433533-18434363	H1-hESC	embryonic stem cell:	n/a	chr11:18433801-18433810
36	E2F6	chr11:18433672-18434161	H1-hESC	embryonic stem cell:	n/a	chr11:18433801-18433810

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18416054..18417892-chr11:18432317..18434579,2	K562	blood:
2	chr11:18415873..18420206-chr11:18430045..18435036,6	MCF-7	breast:
3	chr11:18432193..18433875-chr11:18547475..18550164,2	MCF-7	breast:
4	chr11:18423297..18429050-chr11:18429237..18433863,11	K562	blood:

No data

Variant related genes	Relation type
LDHC	TF binding region
ENSG00000074319	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000256006	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10741744	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10766473	0.84[JPT][hapmap]
rs10766475	0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10766478	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832927	0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10832929	0.86[ASN][1000 genomes]
rs10832930	0.92[ASN][1000 genomes]
rs10832931	0.92[ASN][1000 genomes]
rs10832932	0.92[ASN][1000 genomes]
rs10832933	0.89[ASN][1000 genomes]
rs11024636	0.84[JPT][hapmap]
rs1830426	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1881716	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1881717	0.82[CHB][hapmap]
rs1969562	0.90[ASN][1000 genomes]
rs1969563	0.90[ASN][1000 genomes]
rs2037868	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs2249631	0.90[ASN][1000 genomes]
rs2403278	0.84[JPT][hapmap]
rs2403279	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2658566	0.82[CHB][hapmap]
rs2698559	0.82[CHB][hapmap]
rs2698564	0.86[EUR][1000 genomes]
rs3758680	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs3758681	0.84[JPT][hapmap]
rs3758682	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs3758683	0.84[JPT][hapmap]
rs3781641	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs3809097	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809098	0.83[CHB][hapmap]
rs4274186	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs5030621	0.92[ASN][1000 genomes]
rs6486421	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6486425	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7106099	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7111748	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7112492	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7117399	0.84[ASN][1000 genomes]
rs7120485	0.90[ASN][1000 genomes]
rs7121244	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7128549	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7129689	0.84[JPT][hapmap]
rs7130990	0.90[ASN][1000 genomes]
rs7947664	0.92[ASN][1000 genomes]
rs7951953	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS 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	156 gene(s)	inside rSNPs	diseases
2	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs3809096	COPB1	cis	cerebellum	SCAN
rs3809096	LDHC	cis	Thyroid	GTEx
rs3809096	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs3809096	LDHA	cis	cerebellum	SCAN
rs3809096	LDHC	cis	Skin Sun Exposed Lower leg	GTEx
rs3809096	C11orf58	cis	parietal	SCAN
rs3809096	LDHC	cis	Nerve Tibial	GTEx
rs3809096	LDHAL6A	cis	parietal	SCAN
rs3809096	TSG101	cis	lymphoblastoid	seeQTL
rs3809096	SPTY2D1	cis	parietal	SCAN
rs3809096	LDHC	cis	lung	GTEx
rs3809096	LDHC	cis	lymphoblastoid	seeQTL
rs3809096	LDHAL6A	cis	cerebellum	SCAN
rs3809096	LDHC	cis	Adipose Subcutaneous	GTEx
rs3809096	LDHC	cis	cerebellum	SCAN
rs3809096	PLEKHA7	cis	parietal	SCAN
rs3809096	LDHC	cis	Artery Tibial	GTEx
rs3809096	LDHC	cis	parietal	SCAN
rs3809096	LDHC	cis	Muscle Skeletal	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18429600-18434200	Weak transcription	HepG2	liver
2	chr11:18430200-18440200	Weak transcription	K562	blood
3	chr11:18430400-18434200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:18430600-18434000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr11:18430600-18434000	Weak transcription	Fetal Brain Male	brain
6	chr11:18430800-18434400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr11:18432800-18434000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr11:18433200-18434000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr11:18433400-18434000	Enhancers	HMEC	breast
10	chr11:18433400-18434200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:18433400-18434200	Active TSS	Fetal Kidney	kidney
12	chr11:18433400-18434400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr11:18433400-18434400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:18433400-18434400	Active TSS	Stomach Smooth Muscle	stomach
15	chr11:18433600-18434000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:18433600-18434000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:18433600-18434000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:18433600-18434000	Enhancers	Primary B cells from cord blood	blood
19	chr11:18433600-18434000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr11:18433600-18434000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr11:18433600-18434000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr11:18433600-18434000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:18433600-18434000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:18433600-18434000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:18433600-18434000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:18433600-18434000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:18433600-18434000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr11:18433600-18434000	Enhancers	Brain Germinal Matrix	brain
29	chr11:18433600-18434000	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr11:18433600-18434000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr11:18433600-18434000	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr11:18433600-18434000	Enhancers	Fetal Lung	lung
33	chr11:18433600-18434000	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr11:18433600-18434000	Active TSS	Psoas Muscle	Psoas
35	chr11:18433600-18434000	Flanking Active TSS	A549	lung
36	chr11:18433600-18434000	Active TSS	HSMM	muscle
37	chr11:18433600-18434200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr11:18433600-18434200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
39	chr11:18433600-18434200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:18433600-18434200	Active TSS	Primary T cells from cord blood	blood
41	chr11:18433600-18434200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr11:18433600-18434200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:18433600-18434200	Flanking Active TSS	Liver	Liver
44	chr11:18433600-18434200	Active TSS	Brain Anterior Caudate	brain
45	chr11:18433600-18434200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:18433600-18434200	Active TSS	Fetal Brain Female	brain
47	chr11:18433600-18434200	Flanking Active TSS	Placenta	Placenta
48	chr11:18433600-18434200	Flanking Active TSS	NHEK	skin
49	chr11:18433600-18434200	Active TSS	NHLF	lung
50	chr11:18433600-18434200	Flanking Active TSS	Osteobl	bone

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