Variant report

Variant	rs277649
Chromosome Location	chr3:100067468-100067469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100066721..100069295-chr3:100070418..100073671,4	MCF-7	breast:
2	chr3:100053326..100055313-chr3:100067036..100069328,3	MCF-7	breast:
3	chr3:100062699..100065082-chr3:100066080..100068778,2	K562	blood:
4	chr3:100052307..100055208-chr3:100067208..100069236,3	K562	blood:
5	chr3:100064881..100067551-chr3:100115923..100118439,2	MCF-7	breast:
6	chr3:100057791..100061321-chr3:100063708..100069038,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1036769	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11711112	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];0.84[TSI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1214374	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12696105	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]
rs2289503	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289504	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277621	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277627	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs277631	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277640	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277646	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs378535	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs421855	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4928171	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781422	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784494	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs277649	NIT2	cis	cerebellum	SCAN
rs277649	NIT2	cis	Artery Tibial	GTEx
rs277649	LNP1	cis	Esophagus Muscularis	GTEx
rs277649	C3orf26	cis	cerebellum	SCAN
rs277649	NIT2	cis	parietal	SCAN
rs277649	LNP1	cis	Muscle Skeletal	GTEx
rs277649	TBC1D23	cis	Muscle Skeletal	GTEx
rs277649	RG9MTD1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
3	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:100054800-100067600	Weak transcription	Colonic Mucosa	Colon
5	chr3:100054800-100068600	Weak transcription	Pancreas	Pancrea
6	chr3:100054800-100069000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
9	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:100055000-100068200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:100055000-100068600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:100055200-100068200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:100055200-100071000	Weak transcription	HepG2	liver
15	chr3:100057000-100069200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:100057000-100069600	Strong transcription	Dnd41	blood
17	chr3:100057200-100069200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:100057200-100069600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:100057400-100069600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:100057600-100069200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr3:100057600-100069600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr3:100057600-100069600	Strong transcription	Adipose Nuclei	Adipose
23	chr3:100057800-100069600	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:100057800-100071400	Weak transcription	Fetal Heart	heart
25	chr3:100058000-100069600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:100058000-100069600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:100058000-100069600	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:100058200-100069600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:100058200-100069600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:100059200-100067600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:100059400-100069600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr3:100060000-100069600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:100060200-100067800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:100060200-100068400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:100060200-100069600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:100061000-100068600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr3:100061000-100069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:100061000-100069600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:100061000-100069600	Strong transcription	Liver	Liver
40	chr3:100061200-100068600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:100061200-100069200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:100061400-100069000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:100062600-100069000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:100062600-100069600	Strong transcription	Primary B cells from cord blood	blood
45	chr3:100062600-100069600	Strong transcription	Brain Anterior Caudate	brain
46	chr3:100062600-100069600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr3:100062800-100069200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:100062800-100069600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:100062800-100069600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:100062800-100069600	Strong transcription	Brain Inferior Temporal Lobe	brain

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