Variant report

Variant	rs835636
Chromosome Location	chr3:136674500-136674501
allele	G/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	SP1	chr3:136674419-136675176	HCT-116	colon:	n/a	n/a
2	FOSL1	chr3:136674492-136675294	HCT-116	colon:	n/a	chr3:136674875-136674886 chr3:136674874-136674882
3	TCF7L2	chr3:136674311-136674583	PANC-1	pancreas:	n/a	chr3:136674410-136674420 chr3:136674407-136674421 chr3:136674409-136674418 chr3:136674406-136674422 chr3:136674406-136674422
4	JUND	chr3:136674316-136675226	HCT-116	colon:	n/a	chr3:136674872-136674883 chr3:136674875-136674886 chr3:136674874-136674882
5	JUND	chr3:136674475-136675115	HCT-116	colon:	n/a	chr3:136674872-136674883 chr3:136674875-136674886 chr3:136674874-136674882
6	SP1	chr3:136674447-136675279	HCT-116	colon:	n/a	n/a
7	CBX3	chr3:136674444-136675118	HCT-116	colon:	n/a	n/a
8	POLR2A	chr3:136673083-136675804	K562	blood:	n/a	n/a
9	RCOR1	chr3:136673715-136675470	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:136670796..136672304-chr3:136673206..136674953,2	MCF-7	breast:
2	chr3:136663065..136665134-chr3:136673779..136675884,2	K562	blood:
3	chr3:136670286..136672672-chr3:136673441..136676045,3	K562	blood:

Variant related genes	Relation type
IL20RB	TF binding region
ENSG00000158092	Chromatin interaction
ENSG00000174564	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10470440	0.83[MKK][hapmap]
rs1052618	0.83[MKK][hapmap]
rs108858	1.00[CHD][hapmap]
rs11711599	1.00[CHD][hapmap]
rs12054220	1.00[CHD][hapmap]
rs12629000	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13077864	0.83[ASN][1000 genomes]
rs13095028	0.90[CHD][hapmap]
rs1347209	0.85[CEU][hapmap];0.85[MKK][hapmap]
rs1406539	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1406540	0.85[MKK][hapmap]
rs1433318	0.86[MKK][hapmap]
rs1433319	0.85[MKK][hapmap]
rs1569228	0.85[MKK][hapmap]
rs16844241	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs171519	1.00[CHD][hapmap]
rs1805300	0.86[MKK][hapmap]
rs1914048	0.89[MKK][hapmap]
rs1965107	0.87[ASN][1000 genomes]
rs2031029	0.85[MKK][hapmap]
rs2117009	0.85[CEU][hapmap];0.85[MKK][hapmap]
rs2176270	0.83[ASN][1000 genomes]
rs361232	1.00[CHD][hapmap]
rs361233	1.00[CHD][hapmap]
rs361235	1.00[CHD][hapmap]
rs361240	1.00[CHD][hapmap]
rs361253	1.00[CHD][hapmap]
rs3772388	0.85[MKK][hapmap]
rs4678271	0.83[ASN][1000 genomes]
rs4678274	0.86[MKK][hapmap]
rs4678275	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4678441	0.84[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs4678447	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs62410363	0.83[ASN][1000 genomes]
rs62410438	0.83[ASN][1000 genomes]
rs6439672	0.86[MKK][hapmap]
rs6766755	0.85[MKK][hapmap]
rs6783999	0.85[MKK][hapmap]
rs6786302	0.85[MKK][hapmap]
rs6803618	0.85[CEU][hapmap];0.85[MKK][hapmap]
rs71630059	0.83[ASN][1000 genomes]
rs7610507	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7631541	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7645773	0.85[MKK][hapmap]
rs7648198	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7648817	0.85[MKK][hapmap]
rs835637	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs835649	0.88[ASW][hapmap];0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9289523	0.85[CEU][hapmap]
rs9682106	0.89[MKK][hapmap]
rs9682783	1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs9815771	0.85[MKK][hapmap]
rs9818397	0.85[MKK][hapmap]
rs9819572	0.85[MKK][hapmap]
rs9827648	0.85[MKK][hapmap]
rs9828009	0.85[CEU][hapmap];0.83[MKK][hapmap]
rs9833952	0.86[MKK][hapmap]
rs9836807	0.85[MKK][hapmap]
rs9837990	0.85[CEU][hapmap]
rs9842577	0.85[MKK][hapmap]
rs9845076	1.00[CHD][hapmap]
rs9845460	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9859810	0.85[CEU][hapmap]
rs9860774	0.85[MKK][hapmap]
rs9878367	0.85[MKK][hapmap]
rs9881139	0.85[CEU][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs835636	PCCB	cis	cerebellum	SCAN
rs835636	TMEM22	cis	cerebellum	SCAN
rs835636	SPSB4	cis	cerebellum	SCAN
rs835636	PCCB	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136656400-136681400	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:136658600-136679400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:136662000-136676600	Weak transcription	Psoas Muscle	Psoas
4	chr3:136662400-136675200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:136662600-136676400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:136662800-136678800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr3:136665200-136676000	Weak transcription	Fetal Lung	lung
8	chr3:136665200-136676800	Weak transcription	Aorta	Aorta
9	chr3:136665200-136680200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:136665400-136679000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:136665400-136680200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:136665400-136680200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:136665600-136680000	Weak transcription	Dnd41	blood
14	chr3:136665600-136689400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:136666600-136680400	Weak transcription	Left Ventricle	heart
16	chr3:136669400-136680200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:136670000-136676600	Enhancers	Hela-S3	cervix
18	chr3:136670600-136676600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:136670600-136676800	Enhancers	HMEC	breast
20	chr3:136671600-136676600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:136671800-136676600	Enhancers	NHEK	skin
22	chr3:136672600-136674600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:136672800-136675600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:136673000-136676200	Enhancers	HepG2	liver
25	chr3:136673200-136674800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:136673200-136675000	Enhancers	Adipose Nuclei	Adipose
27	chr3:136673200-136675600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:136673200-136675600	Enhancers	Esophagus	oesophagus
29	chr3:136673200-136676000	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr3:136673200-136676800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:136673400-136676600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:136673600-136674800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:136673600-136675400	Enhancers	Liver	Liver
34	chr3:136673600-136675400	Enhancers	Placenta	Placenta
35	chr3:136673600-136675600	Enhancers	Fetal Intestine Large	intestine
36	chr3:136673600-136675600	Flanking Active TSS	A549	lung
37	chr3:136673600-136676000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:136673600-136676600	Enhancers	K562	blood
39	chr3:136673800-136674600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr3:136673800-136674800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr3:136673800-136674800	Enhancers	Small Intestine	intestine
42	chr3:136673800-136675000	Enhancers	Colon Smooth Muscle	Colon
43	chr3:136673800-136675000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr3:136673800-136675400	Enhancers	HSMMtube	muscle
45	chr3:136673800-136675400	Enhancers	HUVEC	blood vessel
46	chr3:136673800-136675600	Enhancers	Duodenum Mucosa	Duodenum
47	chr3:136673800-136675600	Enhancers	Fetal Intestine Small	intestine
48	chr3:136673800-136675600	Enhancers	Pancreas	Pancrea
49	chr3:136673800-136675600	Enhancers	Stomach Mucosa	stomach
50	chr3:136673800-136676400	Enhancers	Muscle Satellite Cultured Cells	--

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