Variant report

Variant	rs7418410
Chromosome Location	chr1:10236402-10236403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:10236394-10236508	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
UBE4B	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10492969	0.88[CEU][hapmap]
rs10492971	0.81[CEU][hapmap]
rs10492973	0.81[CEU][hapmap]
rs10864450	0.88[CEU][hapmap]
rs10864453	0.88[CEU][hapmap]
rs11121526	0.85[EUR][1000 genomes]
rs11121551	0.81[CEU][hapmap]
rs12120042	0.81[CEU][hapmap]
rs12120191	0.81[CEU][hapmap]
rs12133617	0.88[CEU][hapmap]
rs12141246	0.81[CEU][hapmap]
rs12757288	0.81[CEU][hapmap]
rs1467653	0.88[CEU][hapmap]
rs1538557	0.81[CEU][hapmap]
rs1556915	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1556916	0.81[CEU][hapmap]
rs1556917	0.81[CEU][hapmap]
rs17034643	0.81[CEU][hapmap]
rs1974293	0.83[EUR][1000 genomes]
rs2027330	0.88[CEU][hapmap]
rs2039778	0.81[CEU][hapmap]
rs2180185	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2182326	0.81[CEU][hapmap]
rs3748575	0.88[CEU][hapmap]
rs4333852	0.81[CEU][hapmap]
rs4475756	0.81[CEU][hapmap]
rs4529713	0.81[CEU][hapmap]
rs4623	0.81[CEU][hapmap]
rs4845930	0.88[CEU][hapmap]
rs4846196	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4846197	0.81[CEU][hapmap]
rs4846198	0.92[CEU][hapmap]
rs4846199	0.88[CEU][hapmap]
rs4846207	0.81[CEU][hapmap]
rs4846209	0.81[CEU][hapmap]
rs4846212	0.81[CEU][hapmap]
rs56221672	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6541080	0.84[CEU][hapmap];0.88[GIH][hapmap];0.80[EUR][1000 genomes]
rs6541085	0.88[CEU][hapmap]
rs6541089	0.80[CEU][hapmap]
rs6661326	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6667639	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6696056	0.81[CEU][hapmap]
rs7546364	0.80[CEU][hapmap]
rs7546368	0.88[CEU][hapmap]
rs7553228	0.81[CEU][hapmap]
rs7553935	0.81[CEU][hapmap]
rs8019	0.81[CEU][hapmap]
rs912962	0.88[CEU][hapmap]
rs912963	0.81[CEU][hapmap]
rs9332414	0.81[CEU][hapmap]
rs946501	0.81[CEU][hapmap]
rs946503	0.81[CEU][hapmap]
rs946504	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522629	chr1:10125765-10239197	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7418410	KIF1B	cis	multi-tissue	Pritchard
rs7418410	MTOR	cis	cerebellum	SCAN
rs7418410	APITD1	cis	parietal	SCAN
rs7418410	GPR153	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10191200-10239600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:10214600-10237000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:10218200-10236600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:10221000-10236600	Strong transcription	Adipose Nuclei	Adipose
5	chr1:10221800-10242200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:10223000-10237800	Weak transcription	Psoas Muscle	Psoas
7	chr1:10224400-10236600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:10224800-10236600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:10226400-10238800	Weak transcription	NHEK	skin
10	chr1:10227600-10236600	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr1:10227600-10236600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:10227600-10236600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:10227800-10236600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:10228000-10236600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:10229600-10237800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:10230200-10237000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:10230400-10245800	Weak transcription	Stomach Mucosa	stomach
18	chr1:10230800-10236800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:10230800-10241200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:10231000-10236600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:10231200-10251600	Weak transcription	Right Atrium	heart
22	chr1:10231400-10242200	Strong transcription	Fetal Intestine Small	intestine
23	chr1:10231800-10239800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:10232000-10239400	Weak transcription	Pancreas	Pancrea
25	chr1:10232400-10239400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:10232600-10238800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:10232800-10238600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:10232800-10246800	Weak transcription	Fetal Kidney	kidney
29	chr1:10233000-10236600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:10233000-10238600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:10233000-10238800	Weak transcription	HUVEC	blood vessel
32	chr1:10233000-10239600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:10233200-10237800	Weak transcription	NHDF-Ad	bronchial
34	chr1:10233200-10238600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:10233200-10238600	Weak transcription	Small Intestine	intestine
36	chr1:10233200-10239000	Weak transcription	K562	blood
37	chr1:10233200-10239400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:10233200-10240200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:10233200-10240200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:10233200-10241800	Weak transcription	A549	lung
41	chr1:10233200-10242400	Weak transcription	Fetal Heart	heart
42	chr1:10233200-10258200	Weak transcription	Hela-S3	cervix
43	chr1:10233400-10238600	Weak transcription	Left Ventricle	heart
44	chr1:10233400-10238800	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:10233400-10238800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:10233400-10239400	Weak transcription	Colonic Mucosa	Colon
47	chr1:10233800-10239200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:10233800-10239600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:10234000-10237800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:10234000-10237800	Weak transcription	Fetal Thymus	thymus

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