Variant report

Variant	rs11834570
Chromosome Location	chr12:49977632-49977633
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49959724..49963152-chr12:49977588..49980958,4	K562	blood:
2	chr12:49976050..49978661-chr12:50015939..50018173,2	MCF-7	breast:
3	chr12:49970745..49972990-chr12:49975161..49977938,2	K562	blood:
4	chr12:49977501..49979153-chr12:49998842..50001223,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNH3-1	chr12:49977345-49979872	NONHSAT028116

Variant related genes	Relation type
ENSG00000257964	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000135436	Chromatin interaction
ENSG00000187778	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11831007	0.96[AFR][1000 genomes]
rs11831673	1.00[YRI][hapmap]
rs11832420	1.00[YRI][hapmap]
rs11835085	1.00[YRI][hapmap]
rs3861577	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs57489906	0.81[AFR][1000 genomes]
rs57905415	1.00[AFR][1000 genomes]
rs58725686	0.83[AFR][1000 genomes]
rs59628479	1.00[AFR][1000 genomes]
rs60263616	0.96[AFR][1000 genomes]
rs7310069	0.81[AFR][1000 genomes]
rs7312037	1.00[YRI][hapmap]
rs7313183	1.00[YRI][hapmap]
rs7960185	1.00[YRI][hapmap]
rs7973011	1.00[YRI][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	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS 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 target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49963000-49979200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:49963000-49979200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:49963000-49982200	Weak transcription	NHLF	lung
4	chr12:49963000-49984800	Weak transcription	Small Intestine	intestine
5	chr12:49963000-50003200	Weak transcription	Aorta	Aorta
6	chr12:49963200-49986800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:49963400-49984800	Weak transcription	Primary B cells from cord blood	blood
8	chr12:49967800-49987400	Weak transcription	Hela-S3	cervix
9	chr12:49968400-49978000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:49971200-49984800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:49972000-49982200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:49973800-49982400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:49974400-49978600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr12:49974400-49982400	Weak transcription	NHDF-Ad	bronchial
15	chr12:49974400-49983000	Weak transcription	Gastric	stomach
16	chr12:49974600-49982600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:49974800-49977800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:49974800-49978000	Weak transcription	Fetal Brain Female	brain
19	chr12:49974800-49978400	Weak transcription	Placenta	Placenta
20	chr12:49974800-49979400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:49974800-49979400	Weak transcription	HUVEC	blood vessel
22	chr12:49974800-49982000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:49974800-49983400	Weak transcription	Colonic Mucosa	Colon
24	chr12:49974800-49984600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:49974800-49984800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:49974800-49984800	Weak transcription	Fetal Thymus	thymus
27	chr12:49974800-49985200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:49974800-49985800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:49974800-49986200	Weak transcription	K562	blood
30	chr12:49974800-49986600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:49974800-49986600	Weak transcription	NH-A	brain
32	chr12:49975000-49979200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:49975000-49979400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:49975000-49979600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:49975000-49982400	Weak transcription	HMEC	breast
36	chr12:49975000-49982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:49975000-49984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:49975000-49986200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr12:49975000-49986400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:49975000-49987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:49975200-49979000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:49975400-49980200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:49975400-49983200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:49975600-49978600	Enhancers	Ovary	ovary
45	chr12:49975800-49977800	Enhancers	Rectal Smooth Muscle	rectum
46	chr12:49976000-49978000	Enhancers	Colon Smooth Muscle	Colon
47	chr12:49976000-49978600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:49976000-49981600	Strong transcription	Primary T cells from cord blood	blood
49	chr12:49976000-49983200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:49976200-49977800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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