Variant report

Variant	rs6767158
Chromosome Location	chr3:141228874-141228875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141217049..141220342-chr3:141227507..141230156,3	K562	blood:
2	chr3:141204659..141211656-chr3:141222227..141233100,16	K562	blood:
3	chr3:141227233..141230914-chr3:141242108..141245460,3	K562	blood:
4	chr3:141205080..141210254-chr3:141227089..141231265,7	K562	blood:
5	chr3:141205728..141207739-chr3:141228586..141230979,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250170	Chromatin interaction
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11711375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11916906	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11917587	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062809	0.81[EUR][1000 genomes]
rs13069717	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1366042	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1493209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1582875	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16851435	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs16851438	0.94[JPT][hapmap]
rs16851441	0.88[JPT][hapmap]
rs16851483	0.88[JPT][hapmap]
rs1863867	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[ASN][1000 genomes]
rs2035935	0.88[JPT][hapmap]
rs2035936	0.81[JPT][hapmap]
rs2042864	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2172471	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2312193	0.92[CEU][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.88[EUR][1000 genomes]
rs2639997	0.88[JPT][hapmap]
rs2639998	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2640017	0.88[JPT][hapmap]
rs295299	0.88[JPT][hapmap]
rs295300	0.81[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap]
rs295320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs295323	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35711802	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732869	0.88[JPT][hapmap]
rs3806646	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821709	0.87[JPT][hapmap]
rs3821710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821712	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683610	0.88[JPT][hapmap]
rs6440013	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440015	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6763498	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776003	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800122	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7612543	0.84[TSI][hapmap]
rs7627807	0.88[JPT][hapmap]
rs7632308	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7643837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289631	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9813177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850416	0.81[TSI][hapmap]
rs9851256	0.87[CEU][hapmap]
rs9878347	0.94[JPT][hapmap];0.91[YRI][hapmap]
rs9879503	0.94[JPT][hapmap];0.91[YRI][hapmap]

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	nsv1006237	chr3:141227525-141300722	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6767158	RASA2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141207000-141235800	Weak transcription	Gastric	stomach
2	chr3:141207000-141255000	Weak transcription	Aorta	Aorta
3	chr3:141207400-141231400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:141207800-141233200	Weak transcription	Fetal Intestine Large	intestine
5	chr3:141207800-141235600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:141208400-141231200	Weak transcription	Fetal Lung	lung
7	chr3:141208400-141232600	Weak transcription	NH-A	brain
8	chr3:141209600-141232400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:141209800-141234200	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:141210400-141248000	Weak transcription	NHLF	lung
11	chr3:141211000-141229400	Weak transcription	NHDF-Ad	bronchial
12	chr3:141211400-141235400	Weak transcription	A549	lung
13	chr3:141216000-141239600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:141217200-141232000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:141217800-141229000	Weak transcription	Fetal Heart	heart
16	chr3:141217800-141229400	Weak transcription	Osteobl	bone
17	chr3:141217800-141235800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:141217800-141258400	Weak transcription	Psoas Muscle	Psoas
19	chr3:141218000-141229600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:141218000-141232400	Weak transcription	HUVEC	blood vessel
21	chr3:141218000-141235400	Weak transcription	NHEK	skin
22	chr3:141218200-141233000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:141218200-141235600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:141218400-141233200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:141218400-141233400	Weak transcription	HMEC	breast
26	chr3:141218600-141229800	Weak transcription	Spleen	Spleen
27	chr3:141218600-141230800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:141218600-141235400	Weak transcription	Brain Germinal Matrix	brain
29	chr3:141218800-141229800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:141218800-141230200	Weak transcription	Right Atrium	heart
31	chr3:141218800-141231200	Weak transcription	Fetal Thymus	thymus
32	chr3:141218800-141235600	Weak transcription	Left Ventricle	heart
33	chr3:141219000-141229200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:141219000-141230600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr3:141219000-141231400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr3:141219000-141233000	Weak transcription	GM12878-XiMat	blood
37	chr3:141219000-141233200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:141219000-141235200	Weak transcription	Hela-S3	cervix
39	chr3:141219000-141235400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:141219000-141235600	Weak transcription	Fetal Intestine Small	intestine
41	chr3:141219200-141230200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr3:141219200-141235200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:141220000-141231200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:141221000-141235600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:141221200-141235400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:141221400-141232400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:141221400-141235000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:141221600-141235600	Weak transcription	Fetal Stomach	stomach
49	chr3:141221800-141235400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:141222200-141229200	Weak transcription	Primary monocytes fromperipheralblood	blood

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