Variant report

Variant	rs16840260
Chromosome Location	chr3:98604596-98604597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98602528..98604913-chr3:98611525..98613667,2	K562	blood:
2	chr3:98603129..98605269-chr3:98618566..98620834,2	MCF-7	breast:
3	chr3:98603937..98606892-chr3:98607336..98610177,2	MCF-7	breast:
4	chr3:98595385..98598220-chr3:98601282..98604965,3	K562	blood:

Variant related genes	Relation type
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10433438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511171	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935564	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708475	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716000	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716007	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716281	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716579	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719660	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914591	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914715	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11916285	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11918243	0.97[ASN][1000 genomes]
rs11918944	0.91[ASN][1000 genomes]
rs11920205	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11920327	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11922078	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923486	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923805	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11928233	0.91[ASN][1000 genomes]
rs12203	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13069458	0.91[ASN][1000 genomes]
rs1440154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1471588	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16846347	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17210963	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs17212369	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17213336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17278047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278278	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17852693	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822017	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1827158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3772100	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55650073	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55662129	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55730510	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55764252	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55988144	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075614	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56290036	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322058	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276861	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276862	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276864	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276869	0.91[ASN][1000 genomes]
rs62276879	0.85[ASN][1000 genomes]
rs62276883	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276884	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276885	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276888	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276909	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6440253	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66517942	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6805605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136038	0.90[EUR][1000 genomes]
rs73136045	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73136048	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73136057	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73136060	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73138004	0.92[EUR][1000 genomes]
rs73138027	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138030	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138048	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138053	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138055	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138058	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73138063	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138082	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140009	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140027	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140032	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7432439	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7614892	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638009	0.91[ASN][1000 genomes]
rs7642785	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644946	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8179927	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs982291	0.91[ASN][1000 genomes]

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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv3441569	chr3:98585311-98607020	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98583400-98611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:98584400-98607200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:98587200-98604600	Weak transcription	Ovary	ovary
4	chr3:98589400-98609200	Weak transcription	Fetal Intestine Large	intestine
5	chr3:98590000-98609600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:98590800-98604600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:98591600-98604600	Weak transcription	Aorta	Aorta
8	chr3:98592600-98604600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:98593800-98604600	Weak transcription	Psoas Muscle	Psoas
10	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
11	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
12	chr3:98595200-98608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:98596200-98606600	Weak transcription	HepG2	liver
14	chr3:98597000-98609000	Weak transcription	Right Ventricle	heart
15	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:98598200-98608400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:98599200-98609400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:98599800-98609000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
20	chr3:98600000-98609600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:98600600-98604800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:98600600-98604800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:98600600-98604800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:98600600-98607200	Weak transcription	Brain Angular Gyrus	brain
25	chr3:98600600-98611200	Weak transcription	Liver	Liver
26	chr3:98600600-98613000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
29	chr3:98602200-98605000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr3:98602200-98608600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:98602200-98613600	Genic enhancers	HSMM	muscle
32	chr3:98602400-98613600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:98602600-98604600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:98602600-98605400	Enhancers	Rectal Smooth Muscle	rectum
35	chr3:98602800-98605400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:98603000-98604800	Transcr. at gene 5' and 3'	NH-A	brain
37	chr3:98603000-98605600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:98603200-98605600	Enhancers	Colon Smooth Muscle	Colon
39	chr3:98603200-98612600	Genic enhancers	NHEK	skin
40	chr3:98603400-98604800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:98603400-98605400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:98603400-98605600	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr3:98603400-98606400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:98603400-98606400	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr3:98603400-98607600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr3:98603600-98604800	Flanking Active TSS	Osteobl	bone
47	chr3:98603600-98605000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:98603600-98605600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr3:98603600-98606200	Enhancers	Adipose Nuclei	Adipose
50	chr3:98603600-98608000	Enhancers	HUES48 Cell Line	embryonic stem cell

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