Variant report

Variant	rs12094504
Chromosome Location	chr1:113068334-113068335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113061676..113064298-chr1:113066222..113068945,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RHOC-3	chr1:113068152-113068733	NONHSAT005244

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10399919	0.85[AFR][1000 genomes]
rs11102490	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102492	1.00[AMR][1000 genomes]
rs11102493	1.00[MEX][hapmap]
rs11102500	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102511	0.82[AFR][1000 genomes]
rs1175632	1.00[MEX][hapmap]
rs1175640	1.00[MEX][hapmap]
rs1175642	1.00[MEX][hapmap]
rs12060267	0.95[AFR][1000 genomes]
rs12069022	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069740	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs12073750	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs12077330	0.85[AFR][1000 genomes]
rs12080006	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082350	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12085734	1.00[MEX][hapmap]
rs12087862	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs12091635	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030350	1.00[MEX][hapmap]
rs17030446	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030451	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030455	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030475	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030592	0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs1936047	1.00[MEX][hapmap]
rs4424506	0.82[YRI][hapmap]
rs58634778	0.85[AFR][1000 genomes]
rs59324334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72982599	0.81[AFR][1000 genomes]
rs72984503	0.85[AFR][1000 genomes]
rs72993070	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72993072	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7542272	1.00[MEX][hapmap]
rs9919308	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113052000-113082600	Weak transcription	Brain Angular Gyrus	brain
2	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
3	chr1:113055800-113085200	Weak transcription	Thymus	Thymus
4	chr1:113057800-113069600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:113058400-113069600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:113058400-113086600	Weak transcription	A549	lung
7	chr1:113058600-113069400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:113058800-113119400	Weak transcription	HepG2	liver
9	chr1:113059200-113071600	Weak transcription	Hela-S3	cervix
10	chr1:113059600-113069600	Weak transcription	Spleen	Spleen
11	chr1:113060200-113069600	Weak transcription	Aorta	Aorta
12	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
13	chr1:113060400-113070400	Weak transcription	HMEC	breast
14	chr1:113061200-113072200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:113061400-113081200	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:113062400-113117400	Weak transcription	Psoas Muscle	Psoas
17	chr1:113063400-113092400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:113064400-113068600	Enhancers	Osteobl	bone
19	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:113064600-113071000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:113065000-113092400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:113065200-113114800	Weak transcription	Small Intestine	intestine
23	chr1:113065400-113068600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:113065400-113069800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:113065400-113114600	Weak transcription	Fetal Brain Male	brain
26	chr1:113065600-113068400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:113065600-113068800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:113065600-113070200	Weak transcription	Fetal Kidney	kidney
29	chr1:113065800-113071000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:113065800-113086200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:113066000-113069800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:113066000-113069800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:113066000-113070000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:113066000-113088800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:113066000-113114600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:113066200-113070200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:113066200-113114400	Weak transcription	Dnd41	blood
39	chr1:113066400-113070600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:113066600-113068400	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:113066600-113068400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:113066600-113068600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:113066600-113081200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr1:113066800-113068400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:113066800-113068400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:113066800-113068800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr1:113066800-113070200	Strong transcription	Brain Cingulate Gyrus	brain
48	chr1:113066800-113070600	Strong transcription	Placenta	Placenta
49	chr1:113066800-113071000	Strong transcription	Brain Germinal Matrix	brain
50	chr1:113066800-113071800	Strong transcription	Liver	Liver

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