Variant report

Variant	rs2297881
Chromosome Location	chr1:10397567-10397568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10269845..10271792-chr1:10397112..10399596,2	MCF-7	breast:
2	chr1:10388606..10392277-chr1:10395512..10398907,3	K562	blood:
3	chr1:10397421..10400219-chr1:10415768..10418232,2	K562	blood:

Variant related genes	Relation type
ENSG00000054523	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1046277	1.00[JPT][hapmap]
rs10492970	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11121524	0.82[JPT][hapmap]
rs12074936	0.82[JPT][hapmap]
rs12090079	1.00[MEX][hapmap]
rs17034569	0.82[JPT][hapmap]
rs17034591	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17034601	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17034615	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17034616	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17034627	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17034655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17034660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17034716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17034766	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034775	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17034849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17035154	1.00[MEX][hapmap]
rs2229688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3737154	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3819096	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41258245	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41274480	0.93[AMR][1000 genomes]
rs4329521	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4846195	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs57661717	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57963032	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59211028	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61508659	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6540935	1.00[MEX][hapmap]
rs72864193	0.85[EUR][1000 genomes]
rs72864196	0.85[EUR][1000 genomes]
rs72865913	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72865916	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72865925	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72865926	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72865927	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72865941	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72865946	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72865961	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72865963	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72865999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72867415	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72867421	0.82[AMR][1000 genomes]
rs72867431	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72867433	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72867438	0.93[AMR][1000 genomes]
rs72867441	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72867455	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72867467	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72867469	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72867481	0.81[EUR][1000 genomes]
rs9783053	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10358800-10407000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:10364600-10431000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:10365200-10398400	Weak transcription	Fetal Heart	heart
4	chr1:10379800-10399400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:10380200-10399800	Weak transcription	Stomach Mucosa	stomach
6	chr1:10380200-10404800	Weak transcription	Psoas Muscle	Psoas
7	chr1:10380400-10399600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:10380400-10436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:10380600-10401000	Weak transcription	A549	lung
10	chr1:10380600-10426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:10381000-10436400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:10385200-10436400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:10386000-10434800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:10386400-10403000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:10386400-10421600	Weak transcription	Hela-S3	cervix
16	chr1:10386600-10399800	Weak transcription	Fetal Lung	lung
17	chr1:10386800-10408600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:10393200-10397800	Strong transcription	Brain Hippocampus Middle	brain
19	chr1:10393200-10415800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:10393200-10431200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:10393400-10402200	Strong transcription	Fetal Stomach	stomach
22	chr1:10393600-10430800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:10393800-10406000	Strong transcription	Placenta	Placenta
24	chr1:10393800-10444600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:10394200-10397800	Strong transcription	Left Ventricle	heart
26	chr1:10394200-10398000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:10394200-10398400	Strong transcription	Brain Cingulate Gyrus	brain
28	chr1:10394200-10398400	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr1:10394200-10398400	Strong transcription	HSMMtube	muscle
30	chr1:10394200-10398800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:10394200-10399600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:10394200-10399800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:10394200-10400600	Strong transcription	Fetal Muscle Leg	muscle
34	chr1:10394200-10409800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:10394200-10410000	Strong transcription	Fetal Brain Female	brain
36	chr1:10394200-10410000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:10394200-10411400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:10394200-10413200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:10394200-10414200	Strong transcription	Brain Germinal Matrix	brain
40	chr1:10394200-10414200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr1:10394200-10415800	Strong transcription	Adipose Nuclei	Adipose
42	chr1:10394200-10415800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:10394200-10441800	Strong transcription	Liver	Liver
44	chr1:10394400-10397600	Strong transcription	Brain Angular Gyrus	brain
45	chr1:10394400-10397800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:10394400-10397800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:10394400-10397800	Strong transcription	Fetal Brain Male	brain
48	chr1:10394400-10397800	Strong transcription	NHDF-Ad	bronchial
49	chr1:10394400-10398000	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr1:10394400-10398000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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