Variant report

Variant	rs6540762
Chromosome Location	chr1:212925857-212925858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212903656..212906475-chr1:212923448..212926257,3	K562	blood:
2	chr1:212867492..212870204-chr1:212923902..212926371,2	K562	blood:
3	chr1:212924762..212928442-chr1:212932501..212935953,4	K562	blood:
4	chr1:212922257..212926037-chr1:212961956..212967117,4	K562	blood:

Variant related genes	Relation type
ENSG00000203705	Chromatin interaction
ENSG00000117697	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10127512	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10127703	0.83[ASN][1000 genomes]
rs10127756	0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1046083	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10863988	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863989	0.81[ASN][1000 genomes]
rs10863997	0.84[CHB][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.83[ASN][1000 genomes]
rs11120001	0.81[ASN][1000 genomes]
rs11120006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120007	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11120010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120017	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11120018	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120029	0.90[GIH][hapmap]
rs11556187	0.81[ASN][1000 genomes]
rs11800642	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11806535	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11808846	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11809232	0.81[ASN][1000 genomes]
rs11810895	0.81[ASN][1000 genomes]
rs11811017	0.88[ASN][1000 genomes]
rs12119531	0.81[ASN][1000 genomes]
rs12125867	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12128410	0.90[GIH][hapmap]
rs12128903	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12129465	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137768	0.83[ASN][1000 genomes]
rs12139618	0.81[ASN][1000 genomes]
rs12145131	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12402370	0.83[ASN][1000 genomes]
rs12404618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409787	0.96[EUR][1000 genomes]
rs12729663	0.83[ASN][1000 genomes]
rs13376317	0.81[AMR][1000 genomes]
rs13376383	0.81[AMR][1000 genomes]
rs1507357	0.84[CHB][hapmap];0.93[GIH][hapmap];0.80[MKK][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1507358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532951	0.90[GIH][hapmap]
rs17019726	0.90[GIH][hapmap];0.87[TSI][hapmap]
rs1857971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2135823	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2174780	0.86[ASN][1000 genomes]
rs2174781	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271148	0.84[CHB][hapmap];0.90[GIH][hapmap];0.86[ASN][1000 genomes]
rs2358899	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28872849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34110137	0.81[ASN][1000 genomes]
rs3738798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3738803	0.93[GIH][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs55840547	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56243109	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57449384	0.83[ASN][1000 genomes]
rs58203936	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59231663	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60308869	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61736926	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6540760	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6657089	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6662981	0.81[ASN][1000 genomes]
rs6664049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6665365	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6670648	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6671866	0.81[ASN][1000 genomes]
rs6681171	0.81[ASN][1000 genomes]
rs6687672	0.84[CHB][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6688238	0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6694190	0.88[CEU][hapmap]
rs6694448	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6700204	0.81[ASN][1000 genomes]
rs6702101	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73081830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73081853	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73081902	0.83[ASN][1000 genomes]
rs73083705	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73083707	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73083727	0.94[AFR][1000 genomes]
rs73083731	0.94[AFR][1000 genomes]
rs73083743	0.81[ASN][1000 genomes]
rs73083749	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7516312	0.84[CHB][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7525518	0.81[ASN][1000 genomes]
rs7527216	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7536456	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7536629	0.81[ASN][1000 genomes]
rs7537598	0.95[ASN][1000 genomes]
rs7538755	0.82[AFR][1000 genomes]
rs7546462	0.81[ASN][1000 genomes]
rs7546754	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7550288	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552880	0.81[ASN][1000 genomes]
rs7552899	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv1005983	chr1:212917531-212947521	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6540762	SLC30A1	cis	parietal	SCAN
rs6540762	IL20	cis	cerebellum	SCAN
rs6540762	BATF3	cis	cerebellum	SCAN
rs6540762	NSL1	cis	parietal	SCAN
rs6540762	TATDN3	cis	Adipose Subcutaneous	GTEx
rs6540762	SNORA16B	cis	cerebellum	SCAN
rs6540762	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212926400	Weak transcription	Esophagus	oesophagus
2	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
3	chr1:212895600-212964600	Weak transcription	Gastric	stomach
4	chr1:212895800-212926200	Weak transcription	Hela-S3	cervix
5	chr1:212898800-212934000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:212899800-212926400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:212900400-212927600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:212900400-212932600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:212900400-212936200	Weak transcription	Aorta	Aorta
10	chr1:212901400-212954000	Weak transcription	NH-A	brain
11	chr1:212902200-212941800	Weak transcription	Fetal Kidney	kidney
12	chr1:212902600-212943600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:212903600-212926400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:212904800-212926200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:212908000-212933200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:212912000-212935800	Weak transcription	K562	blood
17	chr1:212915400-212932600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:212915400-212933400	Weak transcription	Ovary	ovary
19	chr1:212915400-212934400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:212915400-212936000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:212915400-212942000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:212917400-212926400	Weak transcription	Thymus	Thymus
23	chr1:212917600-212931200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:212917800-212926000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:212918400-212929400	Weak transcription	Fetal Stomach	stomach
26	chr1:212918800-212930400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:212919600-212926400	Weak transcription	Right Atrium	heart
28	chr1:212920000-212929200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:212920600-212929400	Weak transcription	Fetal Intestine Small	intestine
30	chr1:212921000-212929400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:212922200-212939600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:212923000-212926200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:212923400-212928600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:212923600-212926200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:212923600-212926200	Weak transcription	Brain Anterior Caudate	brain
36	chr1:212923600-212926200	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:212923600-212927600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:212923600-212927800	Weak transcription	Left Ventricle	heart
39	chr1:212923600-212932800	Weak transcription	Fetal Intestine Large	intestine
40	chr1:212923600-212935400	Weak transcription	Lung	lung
41	chr1:212923600-212956200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
43	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:212923800-212926000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:212923800-212926000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:212923800-212926000	Weak transcription	Brain Substantia Nigra	brain
47	chr1:212923800-212926000	Weak transcription	NHLF	lung
48	chr1:212923800-212926200	Weak transcription	Adipose Nuclei	Adipose
49	chr1:212923800-212926200	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:212923800-212926400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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