Variant report

Variant	rs2246476
Chromosome Location	chr1:156241701-156241702
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	chr1:156241682-156242176	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:156241682-156241704	K562	blood:	n/a	n/a
3	POLR2A	chr1:156241573-156242054	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:156240538..156242970-chr1:156250951..156253274,2	MCF-7	breast:
2	chr1:156235998..156238911-chr1:156239009..156243252,3	MCF-7	breast:
3	chr1:156212445..156215383-chr1:156241215..156243298,2	MCF-7	breast:
4	chr1:156234466..156237804-chr1:156239571..156241829,4	K562	blood:

Variant related genes	Relation type
SMG5	TF binding region
ENSG00000163472	Chromatin interaction
ENSG00000198952	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1800247	0.90[ASN][1000 genomes]
rs2253358	0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2495269	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2540168	0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[ASN][1000 genomes]
rs2540169	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.92[ASN][1000 genomes]
rs2764406	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs2764407	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs2985711	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases
2	nsv1011302	chr1:156081561-156532624	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	380 gene(s)	inside rSNPs	diseases
3	nsv915822	chr1:156226286-156651655	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	367 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2246476	PAQR6	cis	Whole Blood	GTEx
rs2246476	C1orf85	cis	Whole Blood	GTEx
rs2246476	EST1B	cis	multi-tissue	Pritchard
rs2246476	PAQR6	cis	multi-tissue	Pritchard
rs2246476	KPRP	cis	parietal	SCAN
rs2246476	C1orf85	cis	multi-tissue	Pritchard
rs2246476	MGC13102	cis	multi-tissue	Pritchard
rs2246476	FAM189B	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:156211600-156251600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:156217400-156245200	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:156217800-156249000	Strong transcription	Thymus	Thymus
4	chr1:156217800-156250400	Strong transcription	Fetal Intestine Small	intestine
5	chr1:156218000-156249000	Strong transcription	Spleen	Spleen
6	chr1:156218200-156250000	Weak transcription	Right Atrium	heart
7	chr1:156218200-156250400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:156218200-156250400	Strong transcription	Fetal Stomach	stomach
9	chr1:156218600-156246800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:156218600-156250400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:156218800-156245000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:156218800-156245600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:156218800-156249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:156218800-156249200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr1:156218800-156250200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:156218800-156250200	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:156218800-156250400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:156218800-156250400	Strong transcription	Fetal Intestine Large	intestine
19	chr1:156219000-156249800	Strong transcription	Dnd41	blood
20	chr1:156219000-156250400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:156219200-156249200	Strong transcription	Lung	lung
22	chr1:156219200-156249600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:156219200-156250000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:156219200-156250200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:156219200-156250600	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr1:156219400-156249600	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:156219400-156250400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:156220000-156250200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr1:156221000-156250400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:156222000-156250000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:156222400-156248800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:156222400-156249200	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:156222400-156249400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:156222400-156250000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:156222800-156247800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:156225400-156248800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:156225400-156249000	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr1:156225400-156249000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:156225400-156249600	Strong transcription	GM12878-XiMat	blood
40	chr1:156225400-156250200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:156225400-156250400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:156225400-156250400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:156225600-156248800	Strong transcription	Fetal Brain Female	brain
44	chr1:156225600-156249200	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:156225600-156249400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:156225600-156250000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:156225600-156250200	Strong transcription	HUVEC	blood vessel
48	chr1:156225800-156246200	Strong transcription	Adipose Nuclei	Adipose
49	chr1:156225800-156246800	Strong transcription	Primary B cells from cord blood	blood
50	chr1:156226000-156246800	Strong transcription	Gastric	stomach

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