Variant report

Variant	rs6687043
Chromosome Location	chr1:175996260-175996261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10436864	0.90[ASN][1000 genomes]
rs10494495	0.81[YRI][hapmap]
rs10737315	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10753111	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10753112	0.81[YRI][hapmap]
rs10753117	0.81[YRI][hapmap]
rs10798425	0.81[YRI][hapmap]
rs10798427	1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10798428	0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs10798432	0.93[CEU][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10798434	0.80[YRI][hapmap]
rs10798435	0.81[ASN][1000 genomes]
rs10913117	0.81[YRI][hapmap]
rs10913150	0.88[ASW][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap]
rs1155229	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11576471	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12029090	0.87[YRI][hapmap]
rs12038027	0.95[ASN][1000 genomes]
rs1357337	0.82[ASW][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap];0.95[ASN][1000 genomes]
rs2039231	0.94[CEU][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2481627	0.82[ASW][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap]
rs2481641	0.94[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2481642	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2481647	0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs2481651	0.85[ASN][1000 genomes]
rs2481657	0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs2502822	0.81[ASW][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs2502826	0.82[ASW][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs2502832	0.82[ASW][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap]
rs2502834	0.94[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2502835	0.94[CEU][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs2502836	0.88[ASW][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap]
rs2502841	0.88[ASW][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap]
rs2502842	0.86[YRI][hapmap]
rs4129061	0.82[MKK][hapmap];0.85[ASN][1000 genomes]
rs4307526	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4314844	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4409605	0.81[YRI][hapmap]
rs4543747	0.81[ASN][1000 genomes]
rs4652143	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs553852	0.84[YRI][hapmap]
rs6425367	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425368	1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[ASN][1000 genomes]
rs6661828	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6678628	0.81[YRI][hapmap]
rs6678812	0.81[YRI][hapmap]
rs6688211	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704509	1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs704827	0.82[ASW][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap]
rs704832	0.95[GIH][hapmap];0.88[TSI][hapmap]
rs7517351	0.82[ASW][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap];0.90[ASN][1000 genomes]
rs7524972	0.95[ASN][1000 genomes]
rs7536464	0.81[ASN][1000 genomes]
rs7537435	0.90[ASN][1000 genomes]
rs7537480	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539247	0.94[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7545043	1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7545639	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7546538	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7552181	1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[ASN][1000 genomes]
rs7553184	0.94[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs791744	0.83[YRI][hapmap]
rs791801	0.88[ASW][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap]
rs9783047	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]

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

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175953800-175999600	Weak transcription	Colonic Mucosa	Colon
2	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:175973600-176003400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:175974000-176003000	Weak transcription	NH-A	brain
5	chr1:175974600-176014200	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:175975400-176003400	Weak transcription	NHLF	lung
7	chr1:175975800-176016200	Weak transcription	HSMMtube	muscle
8	chr1:175976400-176014400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:175976600-176009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:175978200-176001000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:175978200-176003600	Weak transcription	Small Intestine	intestine
13	chr1:175978200-176007400	Weak transcription	Brain Germinal Matrix	brain
14	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
15	chr1:175978400-175996600	Weak transcription	Left Ventricle	heart
16	chr1:175978400-176001600	Weak transcription	Fetal Lung	lung
17	chr1:175978400-176003000	Weak transcription	HSMM	muscle
18	chr1:175978400-176006800	Weak transcription	Fetal Brain Female	brain
19	chr1:175978400-176007000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:175978400-176007000	Weak transcription	Fetal Kidney	kidney
21	chr1:175978400-176014000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:175978400-176014800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:175978400-176017800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:175978600-176007000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:175978800-176003000	Weak transcription	A549	lung
27	chr1:175979200-176011800	Weak transcription	Brain Anterior Caudate	brain
28	chr1:175979400-176009200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:175979400-176012200	Weak transcription	HepG2	liver
30	chr1:175979600-176001000	Weak transcription	NHEK	skin
31	chr1:175979600-176010600	Weak transcription	Right Ventricle	heart
32	chr1:175979600-176012000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:175979600-176045400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:175979800-176014400	Weak transcription	Brain Substantia Nigra	brain
35	chr1:175980000-176001000	Weak transcription	NHDF-Ad	bronchial
36	chr1:175980200-176028000	Weak transcription	K562	blood
37	chr1:175981400-176009200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:175981600-175999000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:175981600-176001600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:175982000-176009800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:175982200-176003200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:175982200-176009400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:175982200-176009400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:175982200-176012200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:175982600-176003200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:175982800-176002800	Weak transcription	Hela-S3	cervix
47	chr1:175983400-176010600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:175984800-175996600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:175985800-176005400	Weak transcription	GM12878-XiMat	blood
50	chr1:175988000-175997600	Strong transcription	Primary monocytes fromperipheralblood	blood

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