Variant report

Variant	rs6541080
Chromosome Location	chr1:10236039-10236040
allele	A/G
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	POLR2A	chr1:10235894-10236314	K562	blood:	n/a	n/a

Variant related genes	Relation type
UBE4B	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12733312	0.80[JPT][hapmap]
rs1556915	0.84[CEU][hapmap]
rs2180184	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6661326	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs7418410	0.84[CEU][hapmap];0.88[GIH][hapmap];0.80[EUR][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6541080	KIF1B	cis	multi-tissue	Pritchard
rs6541080	KIF1B	trans	brain	seeQTL
rs6541080	APITD1	cis	parietal	SCAN
rs6541080	PRAMEF2	cis	parietal	SCAN
rs6541080	KIF1B	cis	brain	seeQTL

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	chr1:10211200-10236400	Strong transcription	Fetal Stomach	stomach
3	chr1:10214600-10237000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:10216200-10236400	Strong transcription	Placenta	Placenta
5	chr1:10218200-10236600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:10218400-10236200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:10221000-10236400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr1:10221000-10236600	Strong transcription	Adipose Nuclei	Adipose
9	chr1:10221800-10242200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:10222200-10236400	Strong transcription	Stomach Smooth Muscle	stomach
11	chr1:10223000-10237800	Weak transcription	Psoas Muscle	Psoas
12	chr1:10224400-10236600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:10224800-10236600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:10226400-10238800	Weak transcription	NHEK	skin
15	chr1:10227600-10236400	Strong transcription	Primary B cells from cord blood	blood
16	chr1:10227600-10236400	Strong transcription	Primary T cells from cord blood	blood
17	chr1:10227600-10236400	Strong transcription	Fetal Lung	lung
18	chr1:10227600-10236600	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr1:10227600-10236600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:10227600-10236600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:10227800-10236600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:10228000-10236600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr1:10229600-10237800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:10230200-10236400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr1:10230200-10237000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:10230400-10245800	Weak transcription	Stomach Mucosa	stomach
27	chr1:10230800-10236400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:10230800-10236800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:10230800-10241200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:10231000-10236600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:10231200-10236200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:10231200-10236200	Strong transcription	Ovary	ovary
33	chr1:10231200-10251600	Weak transcription	Right Atrium	heart
34	chr1:10231400-10242200	Strong transcription	Fetal Intestine Small	intestine
35	chr1:10231800-10239800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:10232000-10239400	Weak transcription	Pancreas	Pancrea
37	chr1:10232400-10239400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:10232600-10238800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:10232800-10238600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:10232800-10246800	Weak transcription	Fetal Kidney	kidney
41	chr1:10233000-10236600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:10233000-10238600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:10233000-10238800	Weak transcription	HUVEC	blood vessel
44	chr1:10233000-10239600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:10233200-10237800	Weak transcription	NHDF-Ad	bronchial
46	chr1:10233200-10238600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:10233200-10238600	Weak transcription	Small Intestine	intestine
48	chr1:10233200-10239000	Weak transcription	K562	blood
49	chr1:10233200-10239400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:10233200-10240200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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