Variant report

Variant	rs666194
Chromosome Location	chr11:65159382-65159383
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	chr11:65159291-65160830	K562	blood:	n/a	n/a
2	EP300	chr11:65159254-65160416	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65158047..65160155-chr11:65175954..65178054,2	MCF-7	breast:
2	chr11:65156578..65159572-chr11:65170803..65173181,2	K562	blood:
3	chr11:65158543..65160066-chr11:65306253..65308125,2	MCF-7	breast:
4	chr11:65101004..65102696-chr11:65157501..65160139,2	MCF-7	breast:

Variant related genes	Relation type
FRMD8	TF binding region
ENSG00000168056	Chromatin interaction
ENSG00000133884	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2073800	0.84[GIH][hapmap]
rs547221	0.89[GIH][hapmap]
rs578270	0.86[GIH][hapmap]
rs652501	0.82[GIH][hapmap]
rs681309	0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
15	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs666194	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs666194	SLC22A24	cis	parietal	SCAN
rs666194	STX5	cis	parietal	SCAN
rs666194	VWCE	cis	parietal	SCAN
rs666194	RELA	cis	parietal	SCAN
rs666194	SCGB2A2	cis	parietal	SCAN
rs666194	CDK2AP2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65154800-65161000	Weak transcription	Aorta	Aorta
2	chr11:65154800-65164800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:65155000-65162000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:65155400-65159400	Enhancers	Left Ventricle	heart
5	chr11:65155600-65159800	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr11:65155600-65159800	Genic enhancers	Fetal Muscle Leg	muscle
7	chr11:65155600-65161800	Genic enhancers	Spleen	Spleen
8	chr11:65155600-65162400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:65155800-65159600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:65156000-65159800	Genic enhancers	Primary B cells from peripheral blood	blood
11	chr11:65156000-65162200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:65156200-65159800	Genic enhancers	Lung	lung
13	chr11:65156400-65159600	Genic enhancers	Fetal Stomach	stomach
14	chr11:65156600-65159800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
15	chr11:65156600-65169800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr11:65156600-65169800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:65156800-65159400	Genic enhancers	NHEK	skin
18	chr11:65157000-65159400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:65157200-65161400	Weak transcription	Small Intestine	intestine
20	chr11:65157200-65182800	Weak transcription	Psoas Muscle	Psoas
21	chr11:65157400-65159400	Enhancers	Fetal Lung	lung
22	chr11:65157400-65159600	Enhancers	Right Atrium	heart
23	chr11:65157400-65170800	Strong transcription	Thymus	Thymus
24	chr11:65157600-65159800	Enhancers	Pancreas	Pancrea
25	chr11:65157600-65159800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr11:65157600-65167800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:65157600-65169000	Weak transcription	Stomach Mucosa	stomach
28	chr11:65157800-65159600	Weak transcription	Gastric	stomach
29	chr11:65157800-65160000	Weak transcription	Primary T cells from cord blood	blood
30	chr11:65157800-65160000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:65157800-65160800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr11:65157800-65164800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr11:65157800-65164800	Weak transcription	HepG2	liver
34	chr11:65157800-65170800	Weak transcription	K562	blood
35	chr11:65158000-65160400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr11:65158200-65159800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:65158200-65160400	Strong transcription	Fetal Thymus	thymus
38	chr11:65158200-65160800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr11:65158200-65168400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:65158200-65170400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr11:65158400-65159400	Genic enhancers	Fetal Intestine Small	intestine
42	chr11:65158400-65159600	Genic enhancers	GM12878-XiMat	blood
43	chr11:65158400-65160200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr11:65158400-65161600	Weak transcription	Colon Smooth Muscle	Colon
45	chr11:65158400-65167800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:65158400-65168000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:65158400-65169600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:65158600-65159400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:65158600-65159400	Genic enhancers	Stomach Smooth Muscle	stomach
50	chr11:65158600-65163000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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