Variant report

Variant	rs12894046
Chromosome Location	chr14:39570288-39570289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39569453..39572073-chr14:39590270..39592529,2	K562	blood:
2	chr14:39569997..39574883-chr14:39575393..39578347,7	MCF-7	breast:
3	chr14:39570001..39572147-chr14:39582267..39584082,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258591	Chromatin interaction
ENSG00000092208	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10130972	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10133797	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10136536	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10140341	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10141243	0.82[EUR][1000 genomes]
rs10149120	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10151683	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12147991	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12437405	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12883061	0.87[EUR][1000 genomes]
rs12891258	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13379360	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17108846	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2415524	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2737721	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2737729	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2753606	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28379470	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28485301	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28502115	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2869	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28810420	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28856917	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34642409	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34816815	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35035794	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35224434	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35423721	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35992529	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3742354	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3759545	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4143954	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4902405	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902406	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902418	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4902431	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4902435	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4902448	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58554991	0.84[AFR][1000 genomes]
rs58851254	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6571893	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67248626	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7147194	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7153124	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8006879	0.86[ASN][1000 genomes]
rs9322994	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12894046	SIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39554200-39571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:39554800-39571600	Weak transcription	K562	blood
3	chr14:39555200-39571600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:39558800-39571400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr14:39560200-39571000	Weak transcription	Aorta	Aorta
6	chr14:39560400-39571400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:39560400-39571600	Weak transcription	Esophagus	oesophagus
8	chr14:39560400-39571600	Weak transcription	Gastric	stomach
9	chr14:39561000-39570600	Weak transcription	Lung	lung
10	chr14:39561000-39571200	Weak transcription	Colonic Mucosa	Colon
11	chr14:39561000-39571400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr14:39561000-39571400	Weak transcription	Psoas Muscle	Psoas
13	chr14:39561600-39571200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr14:39561600-39571400	Weak transcription	Brain Hippocampus Middle	brain
15	chr14:39561600-39571600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr14:39563400-39571600	Weak transcription	Thymus	Thymus
17	chr14:39564000-39571200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr14:39564400-39570400	Weak transcription	Fetal Brain Female	brain
19	chr14:39564400-39571000	Weak transcription	Brain Angular Gyrus	brain
20	chr14:39564400-39571400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:39564400-39571400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr14:39564600-39571000	Weak transcription	HSMMtube	muscle
23	chr14:39564600-39571400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr14:39564800-39571000	Weak transcription	Brain Substantia Nigra	brain
25	chr14:39564800-39571200	Weak transcription	Fetal Thymus	thymus
26	chr14:39564800-39571200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr14:39564800-39571200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr14:39564800-39571400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr14:39565000-39571000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr14:39565000-39571400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr14:39565000-39571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr14:39565000-39571600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr14:39565200-39570800	Weak transcription	Primary B cells from cord blood	blood
34	chr14:39565200-39570800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr14:39565200-39571000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr14:39565200-39571000	Weak transcription	HSMM	muscle
37	chr14:39565400-39571000	Weak transcription	Fetal Muscle Leg	muscle
38	chr14:39565400-39571000	Weak transcription	NHLF	lung
39	chr14:39565400-39571200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr14:39565400-39571200	Weak transcription	Brain Anterior Caudate	brain
41	chr14:39565400-39571200	Weak transcription	NHDF-Ad	bronchial
42	chr14:39565400-39571400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr14:39565400-39571400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr14:39565400-39571400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:39565400-39571400	Weak transcription	Fetal Kidney	kidney
46	chr14:39565400-39571400	Weak transcription	Placenta	Placenta
47	chr14:39565400-39571400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr14:39565400-39571600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr14:39565400-39571600	Weak transcription	Ovary	ovary
50	chr14:39565600-39570400	Weak transcription	Fetal Stomach	stomach

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