Variant report

Variant	rs12040241
Chromosome Location	chr1:176000113-176000114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175993829..175995685-chr1:175998849..176000529,2	K562	blood:
2	chr1:175998716..176001033-chr1:176006174..176008100,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10494498	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10753112	0.97[GIH][hapmap];0.83[TSI][hapmap]
rs10753117	1.00[GIH][hapmap];0.85[TSI][hapmap]
rs10798425	0.97[GIH][hapmap];0.83[TSI][hapmap]
rs10798442	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10913112	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10913117	0.94[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs10913120	0.81[EUR][1000 genomes]
rs10913124	0.84[EUR][1000 genomes]
rs10913128	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023976	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12029090	0.83[EUR][1000 genomes]
rs12030638	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12033847	1.00[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs12039741	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12047295	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12404596	1.00[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs17354120	1.00[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs2175177	0.97[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs34215167	0.80[EUR][1000 genomes]
rs35846379	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3748618	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4526571	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6673760	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6678812	1.00[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs6688898	0.80[EUR][1000 genomes]
rs7517503	1.00[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv1835152	chr1:175996260-176012807	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12040241	DARS2	cis	parietal	SCAN
rs12040241	RP11-318C24.2	cis	Whole Blood	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:175973600-176003400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:175974000-176003000	Weak transcription	NH-A	brain
4	chr1:175974600-176014200	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:175975400-176003400	Weak transcription	NHLF	lung
6	chr1:175975800-176016200	Weak transcription	HSMMtube	muscle
7	chr1:175976400-176014400	Weak transcription	Brain Angular Gyrus	brain
8	chr1:175976600-176009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:175978200-176001000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:175978200-176003600	Weak transcription	Small Intestine	intestine
12	chr1:175978200-176007400	Weak transcription	Brain Germinal Matrix	brain
13	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
14	chr1:175978400-176001600	Weak transcription	Fetal Lung	lung
15	chr1:175978400-176003000	Weak transcription	HSMM	muscle
16	chr1:175978400-176006800	Weak transcription	Fetal Brain Female	brain
17	chr1:175978400-176007000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:175978400-176007000	Weak transcription	Fetal Kidney	kidney
19	chr1:175978400-176014000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:175978400-176014800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:175978400-176017800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:175978600-176007000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:175978800-176003000	Weak transcription	A549	lung
25	chr1:175979200-176011800	Weak transcription	Brain Anterior Caudate	brain
26	chr1:175979400-176009200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:175979400-176012200	Weak transcription	HepG2	liver
28	chr1:175979600-176001000	Weak transcription	NHEK	skin
29	chr1:175979600-176010600	Weak transcription	Right Ventricle	heart
30	chr1:175979600-176012000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:175979600-176045400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:175979800-176014400	Weak transcription	Brain Substantia Nigra	brain
33	chr1:175980000-176001000	Weak transcription	NHDF-Ad	bronchial
34	chr1:175980200-176028000	Weak transcription	K562	blood
35	chr1:175981400-176009200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:175981600-176001600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:175982000-176009800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:175982200-176003200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:175982200-176009400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:175982200-176009400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:175982200-176012200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:175982600-176003200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:175982800-176002800	Weak transcription	Hela-S3	cervix
44	chr1:175983400-176010600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:175985800-176005400	Weak transcription	GM12878-XiMat	blood
46	chr1:175988400-176009400	Weak transcription	Lung	lung
47	chr1:175989000-176001000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:175989000-176003600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:175989000-176009400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:175989000-176009600	Weak transcription	Esophagus	oesophagus

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