Variant report

Variant	rs6668270
Chromosome Location	chr1:62441225-62441226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10889270	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10889271	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.93[ASN][1000 genomes]
rs10889272	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10889277	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10889278	0.89[ASN][1000 genomes]
rs10889279	0.89[ASN][1000 genomes]
rs11207864	0.91[CHB][hapmap]
rs11207869	0.87[ASN][1000 genomes]
rs11207877	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11207878	0.96[ASN][1000 genomes]
rs12135923	0.85[ASN][1000 genomes]
rs2151124	0.82[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs2251182	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2365735	0.82[ASN][1000 genomes]
rs2482881	0.82[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs2482886	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2482889	0.80[ASN][1000 genomes]
rs2498954	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2498962	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs2498968	0.84[CHD][hapmap]
rs35506226	0.81[ASN][1000 genomes]
rs3737108	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs61775620	0.85[ASN][1000 genomes]
rs6587949	1.00[CHB][hapmap]
rs6698695	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7512525	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs7530734	0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:58 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1110	chr1:62395723-62454435	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
8	nsv437210	chr1:62419727-62448245	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2753481	chr1:62424207-62478878	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1010655	chr1:62427826-62447302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv3693433	chr1:62429665-62448451	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1805048	chr1:62433100-62448451	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1812337	chr1:62433100-62448451	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1814392	chr1:62433100-62448451	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1815127	chr1:62433100-62448451	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv1806702	chr1:62433100-62452173	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv1807506	chr1:62433100-62452173	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1813605	chr1:62433814-62453540	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv10217	chr1:62433904-62453204	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv1009859	chr1:62435767-62447302	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv997843	chr1:62436088-62447302	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv947429	chr1:62436550-62451607	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv1014528	chr1:62436620-62447302	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv1003774	chr1:62436620-62454784	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	esv1811896	chr1:62436742-62453709	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv1004315	chr1:62436855-62447302	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	esv1809443	chr1:62436919-62451704	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv517696	chr1:62436929-62441788	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
29	nsv437211	chr1:62436929-62448245	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	esv1804229	chr1:62436929-62448451	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	esv1805701	chr1:62436929-62448451	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	esv1807890	chr1:62436929-62448451	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	esv1810920	chr1:62436929-62448451	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	esv1810004	chr1:62436942-62451029	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
35	esv1807254	chr1:62436942-62453509	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
36	esv3452290	chr1:62437410-62452563	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
37	esv3452291	chr1:62437410-62452563	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
38	esv10531	chr1:62437799-62452376	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
39	nsv818189	chr1:62437872-62441788	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
40	esv1804205	chr1:62437872-62448451	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
41	esv1806678	chr1:62437872-62448451	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
42	esv1808162	chr1:62437872-62448451	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
43	esv1813198	chr1:62437872-62448451	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
44	esv2421746	chr1:62437872-62450535	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
45	nsv546416	chr1:62437872-62492215	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
46	esv1804196	chr1:62437899-62451229	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
47	esv1805072	chr1:62439219-62447302	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
48	esv1814391	chr1:62439219-62447302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
49	nsv1009926	chr1:62439219-62454784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
50	nsv1011197	chr1:62439219-62457712	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6668270	L1TD1	cis	parietal	SCAN
rs6668270	VPS53	trans	parietal	SCAN
rs6668270	DAB1	cis	cerebellum	SCAN
rs6668270	OMA1	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
2	chr1:62409200-62456000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:62409200-62456800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:62409200-62457000	Weak transcription	Fetal Intestine Large	intestine
5	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
6	chr1:62409400-62458400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:62418200-62446400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:62418400-62441400	Weak transcription	Fetal Kidney	kidney
9	chr1:62419600-62445800	Weak transcription	Left Ventricle	heart
10	chr1:62424200-62494200	Weak transcription	Esophagus	oesophagus
11	chr1:62425000-62441400	Weak transcription	Stomach Mucosa	stomach
12	chr1:62430600-62442200	Weak transcription	Fetal Intestine Small	intestine
13	chr1:62433600-62456800	Weak transcription	NHEK	skin
14	chr1:62433800-62444800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:62433800-62445400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:62434000-62457000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:62434800-62444800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:62438600-62445000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:62440400-62441600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:62440400-62457000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:62440600-62442000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:62440800-62441800	Enhancers	Psoas Muscle	Psoas
23	chr1:62440800-62457000	Weak transcription	Liver	Liver
24	chr1:62441000-62441800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:62441200-62441400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:62441200-62441600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:62441200-62441600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr1:62441200-62441600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr1:62441200-62442000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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