Variant report

Variant	rs989392
Chromosome Location	chr9:101743317-101743318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101739430..101741862-chr9:101743138..101745419,2	K562	blood:
2	chr9:101742011..101744498-chr9:101748952..101750643,2	MCF-7	breast:
3	chr9:101732694..101735644-chr9:101742746..101744409,2	MCF-7	breast:
4	chr9:101743138..101745220-chr9:101746552..101748819,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12005080	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12554684	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1543709	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16918106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16918113	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2900147	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3780624	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4327910	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743307	0.93[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs56997979	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57410362	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59112541	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs989392	C17orf71	trans	cerebellum	SCAN
rs989392	XPA	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101728000-101749400	Weak transcription	Aorta	Aorta
2	chr9:101737800-101760800	Weak transcription	Gastric	stomach
3	chr9:101740000-101746200	Weak transcription	Psoas Muscle	Psoas
4	chr9:101740000-101746400	Weak transcription	Fetal Stomach	stomach
5	chr9:101740400-101746200	Weak transcription	Right Ventricle	heart
6	chr9:101740400-101749200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:101740400-101753400	Weak transcription	Spleen	Spleen
8	chr9:101740400-101756800	Weak transcription	Ovary	ovary
9	chr9:101740600-101745400	Weak transcription	Right Atrium	heart
10	chr9:101740600-101749200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:101740800-101745000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:101740800-101745000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:101740800-101745400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:101740800-101745600	Weak transcription	Placenta	Placenta
15	chr9:101740800-101745600	Weak transcription	Pancreas	Pancrea
16	chr9:101740800-101750200	Weak transcription	Esophagus	oesophagus
17	chr9:101740800-101751400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr9:101741000-101745200	Weak transcription	NHDF-Ad	bronchial
19	chr9:101741200-101745800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:101741800-101746400	Enhancers	Fetal Muscle Leg	muscle
21	chr9:101741800-101748800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:101742000-101743400	Enhancers	HSMMtube	muscle
23	chr9:101742400-101743400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:101742400-101743400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:101742400-101743400	Enhancers	HSMM	muscle
26	chr9:101742600-101746000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:101742800-101743800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:101742800-101745600	Weak transcription	Adipose Nuclei	Adipose
29	chr9:101742800-101748600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:101742800-101750400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:101742800-101754200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:101743000-101744800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:101743000-101745000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr9:101743000-101745400	Weak transcription	HMEC	breast
35	chr9:101743000-101745600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:101743000-101746400	Weak transcription	Left Ventricle	heart
37	chr9:101743200-101743400	Enhancers	Skeletal Muscle Male	skeletal muscle

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