Variant report

Variant	rs12998288
Chromosome Location	chr2:191321904-191321905
allele	C/T
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	MAFK	chr2:191321865-191322391	GM12878	blood:	n/a	chr2:191322167-191322183 chr2:191322167-191322178 chr2:191322167-191322178 chr2:191322167-191322182

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191318515..191323057-chr2:191332501..191335066,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272979	TF binding region
ENSG00000151690	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10174174	0.81[AFR][1000 genomes]
rs10182754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10193212	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10931452	0.91[ASN][1000 genomes]
rs12475614	0.91[ASN][1000 genomes]
rs12613807	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12693574	0.91[ASN][1000 genomes]
rs12693575	0.91[ASN][1000 genomes]
rs13020324	0.90[ASN][1000 genomes]
rs13409841	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2354878	0.91[ASN][1000 genomes]
rs35095338	0.96[ASN][1000 genomes]
rs3811607	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4853507	0.88[ASN][1000 genomes]
rs4853510	0.81[AFR][1000 genomes]
rs4853702	0.91[ASN][1000 genomes]
rs4853705	0.93[ASN][1000 genomes]
rs4853710	0.95[LWK][hapmap];0.84[AFR][1000 genomes]
rs4853711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4853713	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6434391	0.91[ASN][1000 genomes]
rs6707691	0.91[ASN][1000 genomes]
rs7557681	0.91[ASN][1000 genomes]
rs7564829	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7596573	0.91[ASN][1000 genomes]
rs7603607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs9646748	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9646815	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33134	chr2:191318791-191365710	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv962094	chr2:191318806-191324621	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12998288	HIBCH	cis	cerebellum	SCAN
rs12998288	MFSD6	cis	parietal	SCAN
rs12998288	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL
rs12998288	MFSD6	cis	lymphoblastoid	seeQTL
rs12998288	MFSD6	cis	Artery Tibial	GTEx
rs12998288	TMEM194B	cis	Adipose Subcutaneous	GTEx
rs12998288	HIBCH	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191302400-191331000	Weak transcription	A549	lung
2	chr2:191303800-191331600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:191303800-191332600	Weak transcription	Fetal Intestine Large	intestine
4	chr2:191306600-191351000	Weak transcription	Pancreas	Pancrea
5	chr2:191307600-191322600	Weak transcription	Aorta	Aorta
6	chr2:191308000-191328800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:191308800-191327200	Weak transcription	Right Atrium	heart
8	chr2:191309200-191322400	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:191309400-191331400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:191310200-191323600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:191310400-191331600	Weak transcription	Stomach Mucosa	stomach
12	chr2:191311400-191324200	Weak transcription	Fetal Heart	heart
13	chr2:191311600-191331400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:191311800-191324600	Weak transcription	Left Ventricle	heart
15	chr2:191311800-191331400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:191311800-191331400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:191311800-191331600	Weak transcription	Ovary	ovary
18	chr2:191312000-191332400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:191312200-191324400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:191313000-191331400	Weak transcription	HSMMtube	muscle
21	chr2:191313000-191333600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:191313800-191323600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:191314000-191331600	Weak transcription	Fetal Kidney	kidney
24	chr2:191315800-191327400	Weak transcription	Spleen	Spleen
25	chr2:191316600-191323400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:191316600-191324600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:191316600-191325200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:191316600-191331200	Weak transcription	NHLF	lung
29	chr2:191317000-191323600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:191317600-191331600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:191318000-191322800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:191318600-191325200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:191318800-191324600	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:191318800-191324600	Weak transcription	Brain Substantia Nigra	brain
35	chr2:191319400-191322000	Strong transcription	Fetal Brain Female	brain
36	chr2:191319400-191323600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:191319400-191331800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:191319400-191332000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:191319600-191323400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:191320200-191323000	Strong transcription	Fetal Thymus	thymus
41	chr2:191320800-191322600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:191320800-191327800	Strong transcription	Primary T cells from cord blood	blood
43	chr2:191321000-191322000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr2:191321000-191322800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:191321000-191323000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:191321000-191323000	Strong transcription	Thymus	Thymus
47	chr2:191321000-191323200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:191321000-191323400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr2:191321000-191323600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:191321200-191322000	Strong transcription	Esophagus	oesophagus

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