Variant report

Variant	rs1972216
Chromosome Location	chr1:158000740-158000741
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:157998908..158001801-chr1:158002681..158007266,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD1D-3	chr1:158000507-158000956	ENSG00000226520.1

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10430456	0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11264878	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs12025305	0.88[ASN][1000 genomes]
rs12037357	0.97[GIH][hapmap]
rs12039337	0.97[GIH][hapmap]
rs12118340	0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12118455	0.88[ASN][1000 genomes]
rs12134949	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12568166	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16839617	0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs16839627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16839630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16839636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1925038	0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1980765	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4445460	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[YRI][hapmap]
rs4971174	0.82[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4971177	0.89[ASW][hapmap];0.82[CEU][hapmap];0.90[GIH][hapmap];0.96[LWK][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4971179	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs4971180	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs4971181	1.00[ASN][1000 genomes]
rs4971182	1.00[ASN][1000 genomes]
rs4971183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs4971184	1.00[ASN][1000 genomes]
rs5018263	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs6427415	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6661149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs6661160	1.00[ASN][1000 genomes]
rs6664509	1.00[ASN][1000 genomes]
rs6665788	0.89[ASN][1000 genomes]
rs6665898	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6666443	0.82[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6680191	0.82[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6690504	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6692314	0.88[ASN][1000 genomes]
rs6699860	0.86[ASN][1000 genomes]
rs7414379	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7537784	0.82[CEU][hapmap];0.97[GIH][hapmap];0.85[EUR][1000 genomes]
rs7548850	1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7554764	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823720	chr1:157978556-158034017	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr1:157985200-158006000	Weak transcription	Fetal Thymus	thymus
2	chr1:157989400-158007400	Weak transcription	Gastric	stomach
3	chr1:157991800-158002200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:157991800-158007400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:157993000-158007400	Weak transcription	HSMMtube	muscle
6	chr1:157993000-158007600	Weak transcription	Esophagus	oesophagus
7	chr1:157993200-158007400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:157995000-158007800	Weak transcription	Brain Germinal Matrix	brain
9	chr1:157995200-158004200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:157995400-158007600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:157995600-158004400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:157995800-158001000	Weak transcription	Fetal Brain Female	brain
13	chr1:157995800-158005600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:157995800-158007400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:157996000-158001000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:157996000-158007400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:157996000-158007400	Weak transcription	Lung	lung
18	chr1:157996200-158006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:157996200-158007600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:157996200-158007600	Weak transcription	Spleen	Spleen
21	chr1:157996400-158001000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:157996400-158005600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:157996400-158007400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:157996800-158001400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:157997000-158001800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:157997200-158005600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:157997600-158004800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:157997600-158047600	Weak transcription	Dnd41	blood
29	chr1:157998000-158007400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:157998200-158007600	Weak transcription	Left Ventricle	heart
31	chr1:157999000-158000800	Weak transcription	NH-A	brain
32	chr1:157999000-158006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:157999000-158013000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:157999200-158005000	Weak transcription	Ovary	ovary
35	chr1:157999400-158001400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:157999400-158005400	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:157999400-158005400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:158000000-158000800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:158000000-158001200	Strong transcription	NHDF-Ad	bronchial
40	chr1:158000000-158001400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:158000000-158001400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:158000000-158001400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:158000000-158001400	Strong transcription	Placenta	Placenta
44	chr1:158000000-158002400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:158000200-158000800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:158000200-158001000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:158000200-158001400	Strong transcription	HSMM	muscle
48	chr1:158000200-158001800	Strong transcription	A549	lung
49	chr1:158000200-158002000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:158000200-158002200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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