Variant report

Variant	rs1214375
Chromosome Location	chr3:100065632-100065633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100057175..100060153-chr3:100065543..100067180,2	K562	blood:
2	chr3:100053577..100055099-chr3:100063294..100065719,2	MCF-7	breast:
3	chr3:100064881..100067551-chr3:100115923..100118439,2	MCF-7	breast:
4	chr3:100057791..100061321-chr3:100063708..100069038,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1045206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132022	0.81[JPT][hapmap]
rs11714045	0.84[CEU][hapmap];0.87[GIH][hapmap];0.82[EUR][1000 genomes]
rs1214381	0.82[YRI][hapmap]
rs13071905	0.81[CEU][hapmap]
rs13073252	0.81[CEU][hapmap]
rs13082297	0.83[EUR][1000 genomes]
rs1486308	0.84[GIH][hapmap]
rs166747	0.82[YRI][hapmap]
rs2289505	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2289506	0.84[CEU][hapmap];0.87[GIH][hapmap];0.83[EUR][1000 genomes]
rs277620	0.93[YRI][hapmap]
rs277629	0.90[YRI][hapmap]
rs277630	0.90[YRI][hapmap]
rs277634	0.86[YRI][hapmap]
rs277635	0.89[YRI][hapmap]
rs277638	0.86[YRI][hapmap]
rs277642	0.89[YRI][hapmap]
rs35945684	0.83[EUR][1000 genomes]
rs3772693	0.81[CEU][hapmap]
rs392066	0.85[LWK][hapmap];0.80[MKK][hapmap]
rs395399	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432715	0.82[YRI][hapmap]
rs7649598	0.80[CEU][hapmap];0.87[GIH][hapmap]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1214375	NFKBIZ	cis	parietal	SCAN
rs1214375	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs1214375	NIT2	cis	parietal	SCAN
rs1214375	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL
rs1214375	FAM55C	cis	parietal	SCAN
rs1214375	NIT2	cis	Artery Tibial	GTEx
rs1214375	TOMM70A	cis	cerebellum	SCAN
rs1214375	OR5H6	cis	cerebellum	SCAN
rs1214375	PCNP	cis	parietal	SCAN
rs1214375	C3orf26	cis	cerebellum	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	chr3:100054800-100067200	Weak transcription	Esophagus	oesophagus
5	chr3:100054800-100067400	Weak transcription	Small Intestine	intestine
6	chr3:100054800-100067600	Weak transcription	Colonic Mucosa	Colon
7	chr3:100054800-100068600	Weak transcription	Pancreas	Pancrea
8	chr3:100054800-100069000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
11	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:100055000-100068200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:100055000-100068600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:100055200-100068200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:100055200-100071000	Weak transcription	HepG2	liver
17	chr3:100057000-100069200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:100057000-100069600	Strong transcription	Dnd41	blood
19	chr3:100057200-100066800	Strong transcription	HSMM	muscle
20	chr3:100057200-100069200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:100057200-100069600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:100057400-100069600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:100057600-100066200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:100057600-100069200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr3:100057600-100069600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr3:100057600-100069600	Strong transcription	Adipose Nuclei	Adipose
27	chr3:100057800-100066200	Strong transcription	HMEC	breast
28	chr3:100057800-100069600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:100057800-100071400	Weak transcription	Fetal Heart	heart
30	chr3:100058000-100065800	Strong transcription	A549	lung
31	chr3:100058000-100069600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr3:100058000-100069600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:100058000-100069600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:100058200-100065800	Strong transcription	Placenta	Placenta
35	chr3:100058200-100069600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:100058200-100069600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:100058400-100065800	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr3:100059200-100067600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:100059400-100069600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:100060000-100069600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:100060200-100067800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:100060200-100068400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:100060200-100069600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:100060800-100066400	Weak transcription	Right Ventricle	heart
45	chr3:100061000-100067000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:100061000-100068600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:100061000-100069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:100061000-100069600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:100061000-100069600	Strong transcription	Liver	Liver
50	chr3:100061200-100066800	Weak transcription	Fetal Brain Female	brain

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