Variant report

Variant	rs12696105
Chromosome Location	chr3:100112816-100112817
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	chr3:100097843..100099760-chr3:100112170..100114759,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1036769	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[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711112	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214374	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119686	0.82[AMR][1000 genomes]
rs2289503	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289504	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2316701	0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs277621	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277627	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs277631	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277646	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277648	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277649	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs378535	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs421855	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928171	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781422	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784494	0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12696105	LNP1	cis	Thyroid	GTEx
rs12696105	LNP1	cis	Esophagus Muscularis	GTEx
rs12696105	LNP1	cis	Muscle Skeletal	GTEx
rs12696105	LOC348801	Cis_1M	lymphoblastoid	RTeQTL
rs12696105	C3orf26	cis	cerebellum	SCAN
rs12696105	RG9MTD1	cis	parietal	SCAN
rs12696105	NIT2	cis	parietal	SCAN
rs12696105	NIT2	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100087600-100114600	Weak transcription	Small Intestine	intestine
2	chr3:100090200-100118400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:100091600-100117600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:100099000-100118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:100099800-100117600	Weak transcription	Colonic Mucosa	Colon
6	chr3:100102800-100118200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:100103800-100117600	Weak transcription	Fetal Kidney	kidney
8	chr3:100103800-100118600	Weak transcription	Brain Substantia Nigra	brain
9	chr3:100104000-100117600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:100104200-100114600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:100104200-100117600	Weak transcription	Brain Angular Gyrus	brain
12	chr3:100104200-100117600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:100104200-100117600	Weak transcription	Psoas Muscle	Psoas
14	chr3:100104200-100117600	Weak transcription	Thymus	Thymus
15	chr3:100104200-100117800	Weak transcription	Esophagus	oesophagus
16	chr3:100104200-100118200	Weak transcription	HSMMtube	muscle
17	chr3:100104200-100118600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:100104200-100118600	Weak transcription	Aorta	Aorta
19	chr3:100104400-100117200	Weak transcription	NHEK	skin
20	chr3:100104600-100117600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:100104600-100117600	Weak transcription	Fetal Brain Male	brain
22	chr3:100104600-100118600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:100104800-100117400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:100105000-100115800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:100105200-100117600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:100105200-100118400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:100105200-100118600	Weak transcription	Placenta	Placenta
28	chr3:100105600-100114600	Weak transcription	Hela-S3	cervix
29	chr3:100105800-100114400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:100105800-100118200	Weak transcription	HMEC	breast
31	chr3:100106000-100117600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:100106000-100117800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:100106200-100115400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:100106200-100117400	Weak transcription	Osteobl	bone
35	chr3:100106200-100117800	Weak transcription	NH-A	brain
36	chr3:100106200-100118200	Weak transcription	HUVEC	blood vessel
37	chr3:100106400-100115800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:100106400-100116800	Weak transcription	Left Ventricle	heart
39	chr3:100106400-100117400	Weak transcription	Fetal Heart	heart
40	chr3:100106400-100117800	Weak transcription	Lung	lung
41	chr3:100106400-100117800	Weak transcription	Ovary	ovary
42	chr3:100106400-100118200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:100106600-100117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:100107400-100117000	Weak transcription	Pancreas	Pancrea
45	chr3:100108200-100115000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:100108200-100116800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:100108200-100117400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:100108200-100117600	Weak transcription	Fetal Lung	lung
49	chr3:100108400-100114600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:100108400-100114600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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