Variant report

Variant	rs6741819
Chromosome Location	chr2:7147973-7147974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:7057062..7058871-chr2:7146022..7148519,2	K562	blood:
2	chr2:7147550..7151799-chr2:7153014..7155237,5	MCF-7	breast:
3	chr2:7056133..7058290-chr2:7146268..7148776,3	K562	blood:
4	chr2:7062503..7063110-chr2:7147599..7148579,3	MCF-7	breast:
5	chr2:7142289..7144797-chr2:7147566..7149207,2	K562	blood:
6	chr2:7142289..7146091-chr2:7146579..7150616,5	K562	blood:
7	chr2:7055201..7058278-chr2:7146257..7149807,3	MCF-7	breast:
8	chr2:7145702..7149842-chr2:7151104..7154625,5	K562	blood:

Variant related genes	Relation type
ENSG00000228203	Chromatin interaction
ENSG00000151692	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10495548	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10495549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929458	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898648	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12465410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13393491	1.00[JPT][hapmap]
rs13398488	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13399190	1.00[JPT][hapmap]
rs13418719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1797554	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2292931	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2460404	0.85[AFR][1000 genomes]
rs2460405	0.81[YRI][hapmap]
rs309314	0.81[AFR][1000 genomes]
rs309317	0.87[AFR][1000 genomes]
rs309319	0.87[AFR][1000 genomes]
rs309322	0.86[AFR][1000 genomes]
rs3755509	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414941	0.85[AFR][1000 genomes]
rs443852	0.93[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs447721	0.93[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs4669124	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4669126	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs700943	0.83[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72781779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs771253	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs771256	0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs771257	1.00[JPT][hapmap]
rs771259	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs771263	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs771265	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs771266	0.83[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant related diseases (count:1)

Disease	PMID	Source
Response to antipsychotic treatment	20195266	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6741819	RNF144A	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7101200-7154000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr2:7115800-7148800	Weak transcription	Esophagus	oesophagus
3	chr2:7121400-7148200	Weak transcription	Fetal Intestine Small	intestine
4	chr2:7124000-7157600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:7126800-7148000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:7127200-7154000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:7131000-7167600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:7131400-7150200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:7131400-7162400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:7131600-7154200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:7131600-7154200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:7133800-7150800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:7137200-7149800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:7137400-7160200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:7139600-7149800	Weak transcription	Ovary	ovary
16	chr2:7141800-7151200	Strong transcription	Primary T cells from cord blood	blood
17	chr2:7142600-7163000	Weak transcription	Small Intestine	intestine
18	chr2:7143600-7149200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:7143800-7149200	Enhancers	Primary hematopoietic stem cells	blood
20	chr2:7143800-7150400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:7144000-7148000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:7144200-7154600	Weak transcription	HepG2	liver
23	chr2:7144400-7150400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:7145000-7150600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:7145200-7148400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr2:7145200-7156200	Enhancers	Brain Angular Gyrus	brain
27	chr2:7145400-7148200	Enhancers	Fetal Brain Male	brain
28	chr2:7145600-7148200	Genic enhancers	Dnd41	blood
29	chr2:7146400-7151200	Enhancers	Left Ventricle	heart
30	chr2:7146400-7153000	Enhancers	Right Ventricle	heart
31	chr2:7146600-7148200	Enhancers	Right Atrium	heart
32	chr2:7146600-7148600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:7146600-7148800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:7146600-7149000	Enhancers	Spleen	Spleen
35	chr2:7146600-7152800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:7146800-7148000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:7146800-7148400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:7146800-7149200	Enhancers	Lung	lung
39	chr2:7146800-7149400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:7146800-7150600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr2:7146800-7151200	Enhancers	Pancreas	Pancrea
42	chr2:7146800-7151200	Enhancers	Psoas Muscle	Psoas
43	chr2:7146800-7156000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:7147000-7148600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:7147000-7148600	Enhancers	Primary B cells from cord blood	blood
46	chr2:7147000-7148800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:7147000-7148800	Enhancers	Brain Germinal Matrix	brain
48	chr2:7147000-7149000	Enhancers	Fetal Lung	lung
49	chr2:7147000-7154800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:7147200-7148000	Enhancers	K562	blood

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