Variant report

Variant	rs10140341
Chromosome Location	chr14:39553959-39553960
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	chr14:39552215..39554960-chr14:39566329..39568969,2	K562	blood:
2	chr14:39544544..39547535-chr14:39553591..39556378,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10136536	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10141471	0.88[ASN][1000 genomes]
rs11157041	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12164875	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12879229	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12883061	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12885242	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12894046	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1555257	0.89[ASN][1000 genomes]
rs17108728	0.88[ASN][1000 genomes]
rs2415524	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28485301	0.80[AMR][1000 genomes]
rs28502115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28699217	0.92[ASN][1000 genomes]
rs28810420	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34642409	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34676226	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34816815	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34985331	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35035794	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35224434	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35423721	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35992529	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36161173	0.91[ASN][1000 genomes]
rs3742354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742355	0.92[ASN][1000 genomes]
rs3759545	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4902308	0.92[ASN][1000 genomes]
rs4902405	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4902406	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6571892	0.83[AFR][1000 genomes]
rs6571893	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71407775	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7152746	0.92[ASN][1000 genomes]
rs7153124	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73285796	0.83[AFR][1000 genomes]
rs8012820	0.83[AFR][1000 genomes]
rs9322992	0.82[EUR][1000 genomes];0.92[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
rs10140341	SIP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39525600-39565600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr14:39526000-39557200	Strong transcription	Osteobl	bone
3	chr14:39526400-39563200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr14:39526800-39554000	Weak transcription	Aorta	Aorta
5	chr14:39526800-39554000	Weak transcription	Esophagus	oesophagus
6	chr14:39526800-39554200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:39526800-39554200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:39526800-39566600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr14:39527000-39554200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:39527000-39565400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr14:39527600-39554200	Weak transcription	K562	blood
12	chr14:39528000-39565400	Strong transcription	Placenta	Placenta
13	chr14:39528000-39565600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr14:39528600-39566400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:39529200-39559400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr14:39529200-39566600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr14:39529600-39564200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr14:39529800-39554200	Weak transcription	Fetal Brain Male	brain
19	chr14:39529800-39566400	Weak transcription	Fetal Heart	heart
20	chr14:39531200-39569200	Weak transcription	Stomach Mucosa	stomach
21	chr14:39532000-39565400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr14:39534200-39566600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr14:39534600-39554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr14:39534600-39566800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr14:39536000-39554200	Weak transcription	Pancreas	Pancrea
26	chr14:39538200-39565200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr14:39538200-39565200	Strong transcription	HUVEC	blood vessel
28	chr14:39538600-39566400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr14:39538800-39556600	Strong transcription	Adipose Nuclei	Adipose
30	chr14:39538800-39561000	Strong transcription	Fetal Muscle Leg	muscle
31	chr14:39539000-39566600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr14:39539200-39565400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr14:39539400-39554000	Weak transcription	Brain Hippocampus Middle	brain
34	chr14:39540400-39559800	Strong transcription	HepG2	liver
35	chr14:39540800-39559600	Strong transcription	Liver	Liver
36	chr14:39541800-39554400	Weak transcription	Psoas Muscle	Psoas
37	chr14:39542200-39554200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr14:39542200-39554200	Weak transcription	Spleen	Spleen
39	chr14:39543200-39556600	Strong transcription	HSMM	muscle
40	chr14:39543400-39554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr14:39543600-39554200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr14:39543600-39554200	Weak transcription	Brain Substantia Nigra	brain
43	chr14:39545200-39554600	Weak transcription	HMEC	breast
44	chr14:39545400-39562800	Strong transcription	GM12878-XiMat	blood
45	chr14:39546600-39556200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr14:39546600-39557600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr14:39546600-39565400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr14:39546800-39556800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr14:39546800-39556800	Strong transcription	Primary T cells from cord blood	blood
50	chr14:39546800-39557000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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