Variant report

Variant	rs10497377
Chromosome Location	chr2:172926226-172926227
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	chr2:172863381..172865132-chr2:172924958..172927915,2	MCF-7	breast:
2	chr2:172920303..172928510-chr2:172947424..172952310,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HAT1-1	chr2:172926226-172926722	NONHSAT075485
2	lnc-HAT1-1	chr2:172926226-172926383	NONHSAT075484
3	lnc-HAT1-1	chr2:172926226-172926383	NONHSAT075486

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction
ENSG00000172878	Chromatin interaction
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10167594	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10171214	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10203462	0.91[ASN][1000 genomes]
rs10209911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1038564	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10930503	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11892858	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs12052482	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12328877	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616766	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622144	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622385	0.85[AMR][1000 genomes]
rs13403822	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs1344393	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17581481	1.00[MKK][hapmap];0.85[AMR][1000 genomes]
rs17581509	1.00[MKK][hapmap];0.85[AMR][1000 genomes]
rs17581610	1.00[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs17615352	0.85[AMR][1000 genomes]
rs17615589	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615607	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796058	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs56923699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57377675	0.85[AMR][1000 genomes]
rs57656367	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6751078	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs73976544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73976547	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs788164	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv875412	chr2:172903124-172942448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv963937	chr2:172925766-172929014	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172911000-172930000	Weak transcription	Primary T cells from cord blood	blood
2	chr2:172911200-172947200	Weak transcription	HSMM	muscle
3	chr2:172914000-172937000	Weak transcription	Pancreas	Pancrea
4	chr2:172917200-172927200	Weak transcription	Left Ventricle	heart
5	chr2:172917200-172927200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:172917400-172927000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:172917400-172934800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:172917800-172927800	Weak transcription	Ovary	ovary
9	chr2:172917800-172932000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:172917800-172944800	Weak transcription	Brain Substantia Nigra	brain
11	chr2:172918000-172930400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:172918000-172932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:172918600-172927200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:172918600-172935600	Weak transcription	Fetal Kidney	kidney
15	chr2:172918600-172935800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:172921200-172927000	Weak transcription	K562	blood
17	chr2:172921800-172937200	Weak transcription	HepG2	liver
18	chr2:172923600-172939800	Weak transcription	Psoas Muscle	Psoas
19	chr2:172924200-172935800	Weak transcription	Adipose Nuclei	Adipose
20	chr2:172924400-172931400	Weak transcription	Primary B cells from cord blood	blood
21	chr2:172925400-172927000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:172925600-172926400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:172925600-172931000	Weak transcription	HSMMtube	muscle
24	chr2:172925600-172932400	Weak transcription	Dnd41	blood
25	chr2:172925800-172927200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:172925800-172930200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:172925800-172937200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:172925800-172937400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:172925800-172942400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:172926000-172928200	Weak transcription	Spleen	Spleen
31	chr2:172926000-172931000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:172926000-172932000	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:172926200-172926400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:172926200-172926400	Enhancers	Brain Germinal Matrix	brain
35	chr2:172926200-172928200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:172926200-172933200	Weak transcription	Aorta	Aorta
37	chr2:172926200-172933400	Weak transcription	Right Ventricle	heart

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