Variant report

Variant	rs805341
Chromosome Location	chr2:54192157-54192158
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54190729..54192357-chr2:54239475..54241800,2	MCF-7	breast:
2	chr2:54188266..54193064-chr2:54193123..54200059,18	K562	blood:
3	chr2:54190368..54192266-chr2:54196698..54199414,2	MCF-7	breast:
4	chr16:10837813..10838339-chr2:54191861..54192361,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10084355	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10201364	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1058320	0.88[CEU][hapmap]
rs1075265	0.89[CEU][hapmap]
rs11683654	0.93[CHB][hapmap]
rs12713253	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13414393	0.86[CHB][hapmap];0.94[CHD][hapmap]
rs1363062	0.96[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1363063	0.89[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1421617	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17268179	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2111868	0.96[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2287642	0.89[CEU][hapmap]
rs2884254	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2909460	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671872	0.81[CEU][hapmap]
rs6545376	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545378	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6545388	0.81[CEU][hapmap]
rs6724389	0.89[CEU][hapmap]
rs6749817	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs698858	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs718872	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7566894	0.81[CEU][hapmap]
rs7569214	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7569370	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7571086	0.81[ASN][1000 genomes]
rs805308	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805309	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805322	0.92[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap]
rs805335	0.89[ASN][1000 genomes]
rs805342	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805343	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805345	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805359	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs805360	0.87[CHB][hapmap];0.85[CHD][hapmap]
rs805366	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs805367	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs805373	0.81[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs805374	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs805375	0.81[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap]
rs805410	0.85[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs805412	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs805423	0.81[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap]
rs805438	0.92[CEU][hapmap];0.83[MEX][hapmap]
rs805439	0.92[CEU][hapmap];0.83[MEX][hapmap]
rs805450	0.80[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805453	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs918357	0.89[CEU][hapmap]
rs929734	0.89[CEU][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs805341	ACYP2	cis	cerebellum	SCAN
rs805341	ACYP2	cis	Muscle Skeletal	GTEx
rs805341	C2orf73	cis	cerebellum	SCAN
rs805341	MRPL43	trans	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54153400-54194600	Weak transcription	Fetal Brain Male	brain
2	chr2:54159400-54195800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:54174200-54195600	Weak transcription	Thymus	Thymus
4	chr2:54175200-54193000	Weak transcription	Fetal Intestine Small	intestine
5	chr2:54175200-54195400	Weak transcription	Fetal Stomach	stomach
6	chr2:54176200-54194200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:54176200-54194600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:54176200-54195400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:54176200-54195400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:54176200-54196000	Weak transcription	Fetal Thymus	thymus
11	chr2:54176200-54196200	Weak transcription	Placenta	Placenta
12	chr2:54176400-54194800	Weak transcription	NHLF	lung
13	chr2:54176400-54195000	Weak transcription	HSMM	muscle
14	chr2:54176800-54192200	Weak transcription	Hela-S3	cervix
15	chr2:54177000-54194800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:54177400-54194400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:54177800-54195400	Weak transcription	Right Ventricle	heart
18	chr2:54180000-54195400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:54187600-54192600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr2:54188000-54192800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:54188200-54192400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr2:54188200-54192400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr2:54188200-54192400	Enhancers	Brain Substantia Nigra	brain
24	chr2:54188200-54192600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr2:54188200-54192800	Enhancers	Primary T cells from cord blood	blood
26	chr2:54188400-54193000	Enhancers	Primary B cells from cord blood	blood
27	chr2:54188400-54195400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:54188600-54195200	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:54188800-54192200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:54188800-54192200	Weak transcription	Stomach Mucosa	stomach
31	chr2:54188800-54192400	Enhancers	A549	lung
32	chr2:54188800-54195800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr2:54189000-54192400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr2:54189000-54194000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:54189000-54195400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:54189200-54194200	Enhancers	HepG2	liver
37	chr2:54189400-54195400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr2:54189600-54192400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr2:54189600-54192800	Enhancers	H1 Cell Line	embryonic stem cell
40	chr2:54189600-54195600	Weak transcription	Fetal Kidney	kidney
41	chr2:54189800-54192400	Enhancers	HMEC	breast
42	chr2:54189800-54196400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:54190000-54196400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:54190200-54195000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:54190400-54192400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:54190400-54192400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:54190400-54192400	Weak transcription	Left Ventricle	heart
48	chr2:54190400-54192400	Weak transcription	Lung	lung
49	chr2:54190400-54193200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:54190400-54194800	Weak transcription	Ovary	ovary

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