Variant report

Variant	rs6679373
Chromosome Location	chr1:120149517-120149518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF697-3	chr1:120148999-120149695	NONHSAT005569

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1045827	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap]
rs10754416	0.85[CHB][hapmap];0.80[CHD][hapmap];0.83[MEX][hapmap]
rs10802123	0.81[ASN][1000 genomes]
rs1830535	0.85[EUR][1000 genomes]
rs1923025	0.86[EUR][1000 genomes]
rs2281493	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap]
rs346673	0.84[EUR][1000 genomes]
rs346674	0.83[EUR][1000 genomes]
rs346675	0.84[EUR][1000 genomes]
rs346677	0.85[EUR][1000 genomes]
rs346681	0.82[EUR][1000 genomes]
rs3795662	0.83[CHD][hapmap];0.83[MEX][hapmap]
rs3795663	0.83[CHD][hapmap];0.83[MEX][hapmap]
rs413854	0.83[EUR][1000 genomes]
rs4659015	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs699775	0.85[CHB][hapmap];0.83[CHD][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap]
rs7552885	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv2763647	chr1:119929442-120154798	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv2757749	chr1:120016696-120214577	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv2758964	chr1:120016696-120214577	Enhancers ZNF genes & repeats Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv946186	chr1:120091427-120161787	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv2756860	chr1:120098661-120162442	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv999314	chr1:120098719-120156465	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv872177	chr1:120099980-120152082	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv463317	chr1:120107602-120162787	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv547618	chr1:120107602-120162787	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv515644	chr1:120110104-120154603	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv547619	chr1:120110104-120154603	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv872178	chr1:120111002-120150452	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1010046	chr1:120112043-120149517	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv997352	chr1:120114732-120149517	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv2756466	chr1:120114879-120150949	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv1011721	chr1:120115285-120149517	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	esv6843	chr1:120115932-120153729	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv1013637	chr1:120117984-120149517	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv1000806	chr1:120117984-120151576	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv1011491	chr1:120122074-120151576	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv1006447	chr1:120123722-120154798	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	esv3396456	chr1:120124380-120155493	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
28	nsv1013957	chr1:120125308-120151576	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	nsv999416	chr1:120125308-120154798	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	nsv1005272	chr1:120125308-120156051	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
31	esv3379396	chr1:120126720-120157658	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
32	esv2754874	chr1:120126990-120156051	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
33	nsv1010583	chr1:120126990-120156465	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
34	nsv999291	chr1:120129344-120156465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
35	nsv872179	chr1:120131597-120162787	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
36	esv16630	chr1:120142387-120150241	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6679373	P2RX4	trans	parietal	SCAN
rs6679373	HSD3B2	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120115200-120160800	Weak transcription	Gastric	stomach
2	chr1:120135200-120151000	Weak transcription	Fetal Stomach	stomach
3	chr1:120139800-120156600	Weak transcription	Left Ventricle	heart
4	chr1:120141800-120150600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:120145400-120150800	Weak transcription	Fetal Intestine Small	intestine
6	chr1:120146200-120165000	Weak transcription	Aorta	Aorta
7	chr1:120146400-120151000	Weak transcription	Fetal Intestine Large	intestine
8	chr1:120146400-120151600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:120146400-120152800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:120146400-120154600	Weak transcription	Fetal Brain Male	brain
11	chr1:120147000-120156600	Weak transcription	Right Ventricle	heart
12	chr1:120147400-120160800	Weak transcription	Psoas Muscle	Psoas
13	chr1:120148000-120151000	Weak transcription	HUVEC	blood vessel
14	chr1:120148400-120149800	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:120148400-120149800	Enhancers	Lung	lung
16	chr1:120148400-120149800	Enhancers	Ovary	ovary
17	chr1:120148400-120150200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:120148400-120151200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:120148600-120149800	Weak transcription	NHEK	skin
20	chr1:120148800-120149600	Enhancers	Fetal Muscle Leg	muscle
21	chr1:120148800-120149600	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr1:120148800-120149600	Enhancers	Spleen	Spleen
23	chr1:120148800-120149800	Enhancers	Adipose Nuclei	Adipose
24	chr1:120148800-120149800	Enhancers	Right Atrium	heart
25	chr1:120148800-120150000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr1:120148800-120150000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr1:120148800-120151400	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr1:120149000-120149600	Enhancers	Placenta	Placenta
29	chr1:120149000-120149600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:120149000-120149800	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr1:120149000-120150000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:120149000-120150000	Enhancers	Fetal Lung	lung
33	chr1:120149200-120154000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:120149400-120149800	Enhancers	Primary B cells from cord blood	blood
35	chr1:120149400-120156200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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