Variant report

Variant	rs4743307
Chromosome Location	chr9:101764212-101764213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101760174..101761965-chr9:101764160..101766601,2	K562	blood:
2	chr9:101763772..101766220-chr9:101865272..101867903,2	MCF-7	breast:
3	chr9:101760174..101763909-chr9:101764160..101767138,3	K562	blood:
4	chr9:101762797..101765082-chr9:101923950..101926109,2	MCF-7	breast:
5	chr9:101764079..101766905-chr9:101863194..101865168,2	MCF-7	breast:
6	chr9:101759295..101764429-chr9:101866150..101870418,5	K562	blood:

Variant related genes	Relation type
ENSG00000106799	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12005080	0.85[EUR][1000 genomes]
rs12352939	0.83[CHD][hapmap]
rs12554684	0.91[EUR][1000 genomes]
rs1543709	1.00[CEU][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs16918106	0.93[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs16918113	0.88[EUR][1000 genomes]
rs2075662	0.93[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs2900147	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3780624	0.89[EUR][1000 genomes]
rs4327910	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4743303	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs56997979	0.82[EUR][1000 genomes]
rs57410362	0.93[EUR][1000 genomes]
rs59112541	0.93[EUR][1000 genomes]
rs989392	0.93[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv6635	chr9:101728257-101773253	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4743307	XPA	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101760200-101772800	Weak transcription	Aorta	Aorta
2	chr9:101760400-101767400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:101761600-101767400	Weak transcription	Colonic Mucosa	Colon
4	chr9:101761600-101768400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:101761600-101770400	Weak transcription	Fetal Intestine Small	intestine
6	chr9:101761600-101814400	Weak transcription	Gastric	stomach
7	chr9:101761800-101765200	Weak transcription	Fetal Stomach	stomach
8	chr9:101761800-101765400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:101761800-101765400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:101761800-101765600	Weak transcription	Left Ventricle	heart
11	chr9:101761800-101765800	Weak transcription	Ovary	ovary
12	chr9:101761800-101765800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:101761800-101768200	Weak transcription	Spleen	Spleen
14	chr9:101761800-101777800	Weak transcription	Pancreas	Pancrea
15	chr9:101761800-101785200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr9:101762600-101769400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr9:101762800-101764400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:101762800-101764600	Enhancers	K562	blood
19	chr9:101762800-101765400	Enhancers	Primary T cells from cord blood	blood
20	chr9:101762800-101765400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:101762800-101769000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:101762800-101769600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr9:101763000-101764400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr9:101763000-101764600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:101763000-101764600	Enhancers	Fetal Thymus	thymus
26	chr9:101763000-101764800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:101763000-101764800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr9:101763000-101764800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr9:101763000-101765000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:101763000-101765000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr9:101763000-101765000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr9:101763000-101765200	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr9:101763000-101765400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:101763000-101765400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr9:101763000-101765600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:101763000-101765600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:101763000-101765600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:101763000-101765800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:101763200-101764600	Enhancers	Primary hematopoietic stem cells	blood
40	chr9:101763200-101767200	Weak transcription	Right Ventricle	heart
41	chr9:101763400-101764600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:101763400-101766800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:101763600-101764600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr9:101763600-101764600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr9:101763600-101765200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:101763600-101767600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr9:101763600-101778000	Weak transcription	HSMMtube	muscle
48	chr9:101763800-101764800	Weak transcription	HSMM	muscle
49	chr9:101763800-101765000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:101763800-101765200	Weak transcription	Brain Hippocampus Middle	brain

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