Variant report

Variant	rs10497555
Chromosome Location	chr2:180864967-180864968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180863719..180867235-chr2:180869883..180873027,5	MCF-7	breast:
2	chr2:180850802..180852751-chr2:180863607..180865249,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163510	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1046356	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs12613483	0.87[ASN][1000 genomes]
rs12618422	0.87[ASN][1000 genomes]
rs12621365	0.87[ASN][1000 genomes]
rs12623020	0.87[ASN][1000 genomes]
rs12693216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16823586	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs16867114	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs16867119	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs16867125	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16867133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs16867136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[ASN][1000 genomes]
rs16867140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs259808	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs262279	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3768839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3845695	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3845697	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3845702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3907347	0.87[ASN][1000 genomes]
rs3912257	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.82[YRI][hapmap];0.98[ASN][1000 genomes]
rs3914458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4893886	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56213876	0.97[ASN][1000 genomes]
rs6433822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6726846	0.83[ASN][1000 genomes]
rs72958832	0.87[ASN][1000 genomes]
rs72958838	0.86[ASN][1000 genomes]
rs72958887	0.93[ASN][1000 genomes]
rs72960663	0.91[ASN][1000 genomes]
rs72960669	0.92[ASN][1000 genomes]
rs72960671	0.92[ASN][1000 genomes]
rs72960679	0.94[ASN][1000 genomes]
rs818659	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9989852	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv875472	chr2:180696414-181024926	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv875473	chr2:180696414-181055597	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1006598	chr2:180766983-180923051	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv531444	chr2:180796233-181434590	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv834473	chr2:180864256-181030940	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180809400-180871000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:180813400-180868200	Weak transcription	Stomach Mucosa	stomach
3	chr2:180816800-180868400	Weak transcription	Pancreas	Pancrea
4	chr2:180816800-180869000	Weak transcription	Spleen	Spleen
5	chr2:180816800-180870600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:180819000-180871000	Weak transcription	Esophagus	oesophagus
7	chr2:180823400-180870600	Weak transcription	Fetal Intestine Small	intestine
8	chr2:180829600-180871200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:180830800-180871000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:180836800-180870400	Weak transcription	A549	lung
11	chr2:180839800-180870400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:180843000-180870200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:180846800-180867000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:180846800-180869800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:180847600-180866200	Weak transcription	Psoas Muscle	Psoas
16	chr2:180849000-180869600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:180850600-180870800	Weak transcription	HSMMtube	muscle
18	chr2:180851000-180870200	Weak transcription	Hela-S3	cervix
19	chr2:180851600-180870400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:180851800-180870400	Weak transcription	HUVEC	blood vessel
21	chr2:180852000-180865000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:180852200-180870600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:180853200-180868000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:180853600-180869600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:180856600-180870400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:180856800-180865400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:180857200-180870000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:180857200-180870400	Weak transcription	Brain Anterior Caudate	brain
29	chr2:180857200-180870400	Weak transcription	Thymus	Thymus
30	chr2:180857200-180871000	Weak transcription	Lung	lung
31	chr2:180857400-180865800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:180857600-180869800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:180857800-180866000	Weak transcription	Ovary	ovary
34	chr2:180857800-180867000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:180857800-180867200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:180857800-180867800	Weak transcription	Fetal Brain Female	brain
37	chr2:180857800-180870400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:180857800-180870400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:180857800-180870600	Weak transcription	NHLF	lung
40	chr2:180857800-180870800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:180857800-180870800	Weak transcription	Fetal Intestine Large	intestine
42	chr2:180858000-180865200	Weak transcription	HMEC	breast
43	chr2:180858000-180865200	Weak transcription	NHEK	skin
44	chr2:180858000-180866800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:180858000-180867200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:180858000-180868200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:180858000-180869000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:180858000-180869600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:180858000-180869800	Weak transcription	Adipose Nuclei	Adipose
50	chr2:180858000-180869800	Weak transcription	Stomach Smooth Muscle	stomach

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