Variant report

Variant	rs6479010
Chromosome Location	chr9:103087128-103087129
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103085724..103088717-chr9:103090423..103093250,3	K562	blood:
2	chr9:101946689..101947278-chr9:103086884..103087396,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10125785	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10760724	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10819756	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10989049	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10989056	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1930243	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1961367	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3923501	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4128230	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4237194	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4237196	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4446782	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4742783	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4743392	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5029343	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6479009	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6479011	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6479014	0.89[EUR][1000 genomes]
rs7020988	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7021310	0.88[EUR][1000 genomes]
rs7025891	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7036570	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7048601	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7849966	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7860513	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7866850	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7869985	0.89[EUR][1000 genomes]
rs7871702	0.88[EUR][1000 genomes]
rs7874900	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7875775	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs914711	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs944710	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs959893	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9775182	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[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	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1835721	chr9:102991314-103096666	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6479010	INVS	cis	multi-tissue	Pritchard
rs6479010	INVS	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103044600-103102400	Weak transcription	Stomach Mucosa	stomach
2	chr9:103046400-103104000	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:103046600-103092400	Strong transcription	Fetal Thymus	thymus
4	chr9:103051000-103088800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:103057600-103112600	Weak transcription	Fetal Brain Male	brain
6	chr9:103058400-103092200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:103063800-103093400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:103063800-103106000	Weak transcription	Esophagus	oesophagus
9	chr9:103064000-103100000	Weak transcription	Colonic Mucosa	Colon
10	chr9:103064200-103093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:103064800-103104200	Weak transcription	Right Ventricle	heart
12	chr9:103065000-103114200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr9:103065200-103087600	Weak transcription	Brain Anterior Caudate	brain
14	chr9:103065400-103087400	Weak transcription	Psoas Muscle	Psoas
15	chr9:103066200-103087800	Weak transcription	Gastric	stomach
16	chr9:103066200-103088400	Weak transcription	Lung	lung
17	chr9:103066200-103100400	Weak transcription	Aorta	Aorta
18	chr9:103066200-103112600	Weak transcription	Pancreas	Pancrea
19	chr9:103066200-103113200	Weak transcription	Spleen	Spleen
20	chr9:103066200-103113800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr9:103066800-103091600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:103067600-103112400	Weak transcription	Small Intestine	intestine
23	chr9:103068200-103094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:103069200-103095400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:103069400-103094800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:103069800-103092000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:103070000-103093800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:103072200-103113800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:103072400-103087600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:103072600-103087600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:103072600-103091800	Weak transcription	Brain Hippocampus Middle	brain
32	chr9:103072800-103087600	Weak transcription	Adipose Nuclei	Adipose
33	chr9:103073800-103088400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr9:103074000-103113200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:103074600-103087600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:103075200-103088600	Weak transcription	Ovary	ovary
37	chr9:103076600-103097000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:103078400-103088000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:103078400-103100200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr9:103078400-103111200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:103078400-103112200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:103078600-103109000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:103079000-103087600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:103079000-103093000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:103079000-103103600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr9:103079200-103097000	Weak transcription	Thymus	Thymus
47	chr9:103079800-103107600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:103080000-103108400	Weak transcription	HSMMtube	muscle
49	chr9:103080200-103087400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:103080400-103088400	Weak transcription	HUVEC	blood vessel

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