Variant report

Variant	rs14976
Chromosome Location	chr2:85818886-85818887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr2:85818590-85819084	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr2:85818826-85818907	A549	lung:	n/a	n/a
3	POLR2A	chr2:85818882-85818909	K562	blood:	n/a	n/a
4	POLR2A	chr2:85818479-85819061	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr2:85818604-85819309	GM12878	blood:	n/a	n/a
6	GATA2	chr2:85818682-85818962	SH-SY5Y	brain:	n/a	n/a
7	POLR2A	chr2:85818402-85819074	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:85645671..85648604-chr2:85818430..85820163,2	MCF-7	breast:
2	chr2:85765298..85767706-chr2:85816811..85818953,3	MCF-7	breast:
3	chr2:85786482..85790460-chr2:85816178..85820132,9	MCF-7	breast:
4	chr2:85787036..85790013-chr2:85817133..85820348,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF181-1	chr2:85818720-85818987	NONHSAT072022

No data

Variant related genes	Relation type
RNF181	TF binding region
ENSG00000115486	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11891495	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12463933	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1374370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17508809	1.00[JPT][hapmap]
rs17508843	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.86[ASN][1000 genomes]
rs2289976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34623563	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56192500	0.83[ASN][1000 genomes]
rs62166770	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62166779	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843872	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569073	1.00[JPT][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs14976	GGCX	cis	cerebellum	SCAN
rs14976	VAMP5	cis	lymphoblastoid	seeQTL
rs14976	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs14976	GGCX	cis	parietal	SCAN
rs14976	VAMP5	Cis_1M	lymphoblastoid	RTeQTL
rs14976	RNF103	cis	parietal	SCAN
rs14976	VAMP5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85812600-85819200	Enhancers	Fetal Muscle Leg	muscle
2	chr2:85812600-85821200	Weak transcription	Fetal Heart	heart
3	chr2:85812800-85819000	Enhancers	Primary hematopoietic stem cells	blood
4	chr2:85813000-85819600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:85813200-85821400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:85813400-85819000	Enhancers	Right Atrium	heart
7	chr2:85813600-85821400	Weak transcription	Fetal Intestine Large	intestine
8	chr2:85813800-85820000	Weak transcription	Fetal Intestine Small	intestine
9	chr2:85814000-85821600	Weak transcription	Small Intestine	intestine
10	chr2:85814600-85819400	Enhancers	Fetal Lung	lung
11	chr2:85814600-85819600	Enhancers	Left Ventricle	heart
12	chr2:85814600-85819600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:85814800-85819400	Enhancers	Brain Hippocampus Middle	brain
14	chr2:85815000-85821400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:85815000-85821600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:85815200-85819000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:85815200-85819000	Weak transcription	Fetal Stomach	stomach
18	chr2:85815200-85819200	Enhancers	Fetal Muscle Trunk	muscle
19	chr2:85815200-85821600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:85815400-85821200	Weak transcription	Dnd41	blood
21	chr2:85815400-85821400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:85815400-85821400	Weak transcription	GM12878-XiMat	blood
23	chr2:85815600-85819200	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:85815600-85821400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:85815600-85821400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:85815600-85821400	Weak transcription	Hela-S3	cervix
27	chr2:85815800-85819000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr2:85815800-85819000	Enhancers	Ovary	ovary
29	chr2:85815800-85819200	Enhancers	Brain Angular Gyrus	brain
30	chr2:85815800-85821400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr2:85815800-85821600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:85816000-85819200	Enhancers	Brain Substantia Nigra	brain
33	chr2:85816000-85820200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:85816000-85821400	Weak transcription	Fetal Kidney	kidney
35	chr2:85816000-85821400	Weak transcription	Thymus	Thymus
36	chr2:85816200-85819600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:85816200-85821400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:85816400-85819000	Enhancers	Gastric	stomach
39	chr2:85816600-85819600	Enhancers	Colon Smooth Muscle	Colon
40	chr2:85816800-85819000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr2:85817000-85819000	Enhancers	Fetal Thymus	thymus
42	chr2:85817000-85819000	Enhancers	Stomach Smooth Muscle	stomach
43	chr2:85817000-85819600	Enhancers	Spleen	Spleen
44	chr2:85817000-85819800	Enhancers	Stomach Mucosa	stomach
45	chr2:85817200-85819000	Enhancers	Esophagus	oesophagus
46	chr2:85817200-85819000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr2:85817200-85819400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr2:85817400-85819200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:85817600-85819000	Enhancers	Colonic Mucosa	Colon
50	chr2:85817600-85819000	Enhancers	Right Ventricle	heart

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