Variant report

Variant	rs3133168
Chromosome Location	chr4:107252245-107252246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:107246333..107250100-chr4:107250113..107253546,4	K562	blood:
2	chr4:107235692..107241045-chr4:107249153..107254463,7	K562	blood:
3	chr4:107251770..107254380-chr4:107254601..107256779,2	MCF-7	breast:
4	chr4:107246333..107250100-chr4:107250113..107253546,3	K562	blood:
5	chr4:107243504..107246800-chr4:107249107..107253056,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164022	Chromatin interaction
ENSG00000145348	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10000428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10003024	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10004611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10008428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10016884	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10017969	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10018910	0.94[ASN][1000 genomes]
rs10027207	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10049933	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732791	0.89[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931386	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12642691	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12650692	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13101612	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13121614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17272618	0.94[ASN][1000 genomes]
rs2691804	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28467469	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28784652	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28805707	0.94[ASN][1000 genomes]
rs2949625	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2949650	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3018066	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3018069	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3109953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109955	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3109960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3113249	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113250	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113252	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3133169	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4307042	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4314353	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4374692	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4382109	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4508971	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4569824	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4600995	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533242	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6819081	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836198	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6844105	0.94[ASN][1000 genomes]
rs6849573	0.94[ASN][1000 genomes]
rs6852388	0.94[ASN][1000 genomes]
rs7356287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7663321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7667596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7668276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7682646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7692652	0.86[ASN][1000 genomes]
rs7693333	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7693448	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9991203	0.84[ASW][hapmap]
rs9996093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830029	chr4:107203096-107353483	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3133168	TBCK	cis	parietal	SCAN
rs3133168	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs3133168	TBCK	cis	lymphoblastoid	seeQTL
rs3133168	ELOVL6	cis	cerebellum	SCAN
rs3133168	MGC16169	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107238600-107258000	Weak transcription	Gastric	stomach
2	chr4:107238600-107258400	Weak transcription	Spleen	Spleen
3	chr4:107238600-107258600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:107238600-107259600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:107238600-107259600	Weak transcription	Pancreas	Pancrea
6	chr4:107238800-107259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:107239000-107252400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr4:107239000-107252800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:107239000-107259200	Weak transcription	Fetal Brain Male	brain
10	chr4:107239200-107258400	Weak transcription	Aorta	Aorta
11	chr4:107239200-107259400	Weak transcription	Psoas Muscle	Psoas
12	chr4:107239400-107255200	Weak transcription	Stomach Mucosa	stomach
13	chr4:107240800-107253000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:107242200-107258600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:107242800-107257800	Weak transcription	Esophagus	oesophagus
16	chr4:107242800-107258400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:107242800-107259400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:107243400-107257800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:107243400-107258000	Weak transcription	Lung	lung
20	chr4:107243400-107271400	Weak transcription	Right Ventricle	heart
21	chr4:107243800-107259600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:107244000-107255400	Weak transcription	Fetal Stomach	stomach
23	chr4:107244000-107258000	Weak transcription	Small Intestine	intestine
24	chr4:107244200-107258400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:107245600-107259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:107245800-107257600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr4:107245800-107258400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr4:107245800-107259000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:107245800-107261800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr4:107245800-107262200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr4:107245800-107263000	Strong transcription	Dnd41	blood
32	chr4:107246000-107258400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:107246000-107262000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr4:107246200-107254200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:107246200-107255200	Strong transcription	Fetal Lung	lung
36	chr4:107246200-107262000	Strong transcription	NH-A	brain
37	chr4:107246400-107254800	Strong transcription	Primary B cells from cord blood	blood
38	chr4:107246400-107259400	Strong transcription	Placenta	Placenta
39	chr4:107246600-107256200	Strong transcription	HSMM	muscle
40	chr4:107246600-107256400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:107246800-107260200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:107246800-107260800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:107247000-107253400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:107247000-107258600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:107247000-107258800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:107247000-107259600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr4:107247000-107260600	Strong transcription	Adipose Nuclei	Adipose
48	chr4:107247000-107261200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:107247000-107261800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr4:107247000-107262000	Strong transcription	Duodenum Mucosa	Duodenum

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