Variant report

Variant	rs12354943
Chromosome Location	chr10:116190000-116190001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116188336..116192373-chr10:116194440..116198221,4	K562	blood:
2	chr10:116185292..116187942-chr10:116188766..116190675,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VWA2-1	chr10:116189623-116190031	NONHSAT016454

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11196728	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11196738	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196750	0.83[CEU][hapmap]
rs12354693	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355335	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12356147	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12357098	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12359269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12573832	0.81[CEU][hapmap]
rs17406965	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293058	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs475150	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs605654	0.90[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61868314	0.89[EUR][1000 genomes]
rs61868324	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622320	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs622646	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6585277	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6585283	0.80[CEU][hapmap]
rs7069926	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7900888	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910088	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7916374	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916796	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs941855	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9665297	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116180000-116196200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr10:116180800-116190200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:116181000-116190400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:116181400-116190600	Weak transcription	HMEC	breast
5	chr10:116186000-116193600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr10:116186600-116193200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:116186600-116198200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr10:116186800-116194400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr10:116187000-116210400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr10:116187200-116192800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:116187200-116197800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr10:116187200-116203000	Weak transcription	Colon Smooth Muscle	Colon
13	chr10:116187400-116191000	Weak transcription	Fetal Lung	lung
14	chr10:116187400-116192000	Weak transcription	Fetal Muscle Leg	muscle
15	chr10:116187400-116192200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr10:116187400-116194200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr10:116187400-116194400	Weak transcription	Fetal Heart	heart
18	chr10:116187400-116196400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr10:116187400-116198400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr10:116187600-116190000	Weak transcription	Lung	lung
21	chr10:116187600-116193200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr10:116187600-116193800	Weak transcription	Brain Angular Gyrus	brain
23	chr10:116187600-116194400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr10:116187600-116194400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr10:116187600-116198000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr10:116187600-116198400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:116187600-116198600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr10:116187600-116199000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr10:116187600-116204600	Weak transcription	Spleen	Spleen
30	chr10:116187800-116190200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:116187800-116190800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:116187800-116193400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr10:116187800-116193600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr10:116187800-116193800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr10:116187800-116196000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr10:116187800-116198000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr10:116187800-116198000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr10:116187800-116198000	Weak transcription	HSMM	muscle
39	chr10:116187800-116199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:116187800-116207600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr10:116188000-116190000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr10:116188000-116190200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr10:116188000-116191200	Weak transcription	HUVEC	blood vessel
44	chr10:116188000-116191800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr10:116188000-116193600	Weak transcription	Gastric	stomach
46	chr10:116188000-116193800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr10:116188000-116194000	Weak transcription	Ovary	ovary
48	chr10:116188000-116198200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr10:116188000-116198200	Weak transcription	Stomach Mucosa	stomach
50	chr10:116188000-116211000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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