Variant report

Variant	rs10989050
Chromosome Location	chr9:103068934-103068935
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INVS-1	chr9:103068327-103069755	NONHSAT133713

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10819755	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10819757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10819758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819760	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819765	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819766	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819768	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819771	0.91[CEU][hapmap]
rs10819772	0.91[CEU][hapmap]
rs10989041	0.97[EUR][1000 genomes]
rs10989046	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs10989047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989062	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989063	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989068	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989069	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989074	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10989077	1.00[ASN][1000 genomes]
rs11515449	0.96[EUR][1000 genomes]
rs11515542	0.96[EUR][1000 genomes]
rs11788648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790431	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs11791637	0.83[EUR][1000 genomes]
rs11791943	1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793726	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794753	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11795004	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12000794	0.91[CEU][hapmap]
rs12002124	0.91[CEU][hapmap]
rs12003468	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs12005177	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352336	1.00[ASN][1000 genomes]
rs12375859	1.00[ASN][1000 genomes]
rs12379480	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919024	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs3199998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274951	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274961	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62579387	1.00[ASN][1000 genomes]
rs7028101	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036972	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037122	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037419	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039994	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs7849019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866700	0.81[CEU][hapmap];0.95[EUR][1000 genomes]
rs7873560	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874036	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103044200-103071200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:103044600-103102400	Weak transcription	Stomach Mucosa	stomach
3	chr9:103046000-103075400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr9:103046200-103072800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:103046400-103104000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr9:103046600-103092400	Strong transcription	Fetal Thymus	thymus
7	chr9:103047400-103070800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:103048000-103078000	Strong transcription	Primary T cells from cord blood	blood
9	chr9:103048200-103069600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:103048400-103083000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr9:103049000-103073800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:103050600-103069600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr9:103050600-103086400	Strong transcription	Dnd41	blood
14	chr9:103050800-103080400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr9:103051000-103088800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:103051200-103078000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:103051400-103074000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:103053400-103074800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr9:103054600-103069800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:103055800-103077600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr9:103057600-103112600	Weak transcription	Fetal Brain Male	brain
22	chr9:103058400-103092200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr9:103058800-103084800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:103059800-103074400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr9:103061200-103074200	Weak transcription	Brain Germinal Matrix	brain
26	chr9:103061800-103073400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:103062200-103074200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr9:103062600-103069800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:103063800-103093400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:103063800-103106000	Weak transcription	Esophagus	oesophagus
31	chr9:103064000-103100000	Weak transcription	Colonic Mucosa	Colon
32	chr9:103064200-103093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:103064600-103070000	Weak transcription	Fetal Brain Female	brain
34	chr9:103064600-103079400	Weak transcription	HSMMtube	muscle
35	chr9:103064800-103070000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:103064800-103070800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr9:103064800-103104200	Weak transcription	Right Ventricle	heart
38	chr9:103065000-103070800	Weak transcription	Fetal Heart	heart
39	chr9:103065000-103071400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:103065000-103080600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:103065000-103114200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr9:103065200-103087600	Weak transcription	Brain Anterior Caudate	brain
43	chr9:103065400-103069600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:103065400-103080200	Weak transcription	Brain Substantia Nigra	brain
45	chr9:103065400-103087400	Weak transcription	Psoas Muscle	Psoas
46	chr9:103066000-103071200	Weak transcription	HMEC	breast
47	chr9:103066000-103071600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr9:103066200-103070600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr9:103066200-103070600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr9:103066200-103070800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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