Variant report

Variant	rs12078857
Chromosome Location	chr1:151111837-151111838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151111829-151111909	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151040013..151045011-chr1:151111761..151118476,6	MCF-7	breast:

Variant related genes	Relation type
SEMA6C	TF binding region
ENSG00000197622	Chromatin interaction
ENSG00000143458	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11204774	0.82[ASW][hapmap];0.93[YRI][hapmap]
rs11204783	1.00[EUR][1000 genomes]
rs11204794	1.00[MEX][hapmap]
rs11204796	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12064646	1.00[EUR][1000 genomes]
rs12065634	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12067174	0.84[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12068365	0.84[ASW][hapmap];0.87[YRI][hapmap]
rs12074309	0.84[ASW][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs12076626	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12088079	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12088941	1.00[ASW][hapmap];0.86[LWK][hapmap];0.86[YRI][hapmap]
rs12089658	1.00[ASW][hapmap]
rs12090246	0.82[ASW][hapmap];0.93[YRI][hapmap]
rs16832976	0.82[ASW][hapmap];0.87[YRI][hapmap]
rs6587556	1.00[EUR][1000 genomes]
rs6664387	0.84[ASW][hapmap];0.90[MKK][hapmap];0.87[YRI][hapmap]
rs7526955	0.84[ASW][hapmap];0.87[YRI][hapmap]
rs7532854	1.00[EUR][1000 genomes]
rs7537292	0.93[YRI][hapmap]
rs7550809	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs955955	0.84[ASW][hapmap];0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872422	chr1:151098077-151115186	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151079800-151114800	Weak transcription	HSMM	muscle
2	chr1:151104000-151114800	Weak transcription	Psoas Muscle	Psoas
3	chr1:151104400-151116600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:151104400-151117000	Weak transcription	Fetal Kidney	kidney
5	chr1:151104400-151118000	Weak transcription	Aorta	Aorta
6	chr1:151104600-151117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:151104600-151118200	Weak transcription	Primary T cells from cord blood	blood
8	chr1:151104800-151115600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:151105000-151114800	Strong transcription	Fetal Brain Female	brain
10	chr1:151105000-151114800	Weak transcription	Right Atrium	heart
11	chr1:151105000-151115400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:151105000-151115600	Weak transcription	Fetal Thymus	thymus
13	chr1:151105200-151115200	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:151105200-151115400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:151105200-151117000	Weak transcription	Placenta	Placenta
16	chr1:151105400-151117000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:151105600-151112800	Strong transcription	Left Ventricle	heart
18	chr1:151105600-151114800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:151105600-151115800	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:151105600-151118000	Weak transcription	Gastric	stomach
21	chr1:151105800-151113000	Strong transcription	Stomach Smooth Muscle	stomach
22	chr1:151105800-151115600	Weak transcription	Thymus	Thymus
23	chr1:151105800-151117200	Weak transcription	Spleen	Spleen
24	chr1:151106000-151112200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:151106000-151113200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:151106000-151113200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:151106000-151113400	Strong transcription	Fetal Intestine Large	intestine
28	chr1:151106000-151114800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:151106000-151115000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:151106200-151113000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:151106200-151113000	Strong transcription	Fetal Lung	lung
32	chr1:151106200-151116000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:151106600-151112600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr1:151106600-151115400	Strong transcription	Fetal Stomach	stomach
35	chr1:151106600-151116000	Strong transcription	Fetal Intestine Small	intestine
36	chr1:151106800-151113000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:151106800-151113000	Strong transcription	Adipose Nuclei	Adipose
38	chr1:151106800-151113000	Strong transcription	Ovary	ovary
39	chr1:151106800-151114400	Weak transcription	Fetal Heart	heart
40	chr1:151107000-151116600	Weak transcription	HUVEC	blood vessel
41	chr1:151107000-151117600	Weak transcription	Colonic Mucosa	Colon
42	chr1:151107400-151114800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:151107400-151115000	Strong transcription	Brain Germinal Matrix	brain
44	chr1:151107800-151115800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:151108200-151112400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:151108400-151112400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:151108400-151115400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:151108400-151117200	Weak transcription	Brain Substantia Nigra	brain
49	chr1:151108600-151114800	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:151108600-151117800	Weak transcription	Esophagus	oesophagus

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