Variant report

Variant	rs12489397
Chromosome Location	chr3:140696929-140696930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140658522..140661250-chr3:140695108..140698043,2	K562	blood:

Variant related genes	Relation type
ENSG00000114120	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1047330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1056126	0.89[ASN][1000 genomes]
rs1056127	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10935413	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935414	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1109282	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs1109283	1.00[CHB][hapmap]
rs11707116	0.87[ASN][1000 genomes]
rs11710204	0.98[ASN][1000 genomes]
rs11710926	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs11711131	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs11713505	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs11713816	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714438	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs11715248	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs11717620	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs11718040	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs11718539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718563	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs11720342	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs13063450	0.92[EUR][1000 genomes]
rs13099706	0.92[EUR][1000 genomes]
rs1568337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1593623	0.88[EUR][1000 genomes]
rs1593624	0.89[ASN][1000 genomes]
rs16850915	0.87[ASN][1000 genomes]
rs16850917	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs16850921	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs16850924	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs16850926	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs16851001	0.88[EUR][1000 genomes]
rs2042759	0.86[EUR][1000 genomes]
rs2081662	0.92[EUR][1000 genomes]
rs2292919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2310859	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2311491	0.92[EUR][1000 genomes]
rs2555702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871615	0.94[CHB][hapmap]
rs35140461	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755764	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs3755765	0.89[ASN][1000 genomes]
rs3773835	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs3773837	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs3773838	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs4068843	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4524250	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4528914	0.91[EUR][1000 genomes]
rs4538351	0.92[EUR][1000 genomes]
rs57151068	0.89[ASN][1000 genomes]
rs57526660	0.89[ASN][1000 genomes]
rs57799705	0.89[ASN][1000 genomes]
rs59128309	0.89[ASN][1000 genomes]
rs59221985	0.89[ASN][1000 genomes]
rs61151473	1.00[ASN][1000 genomes]
rs61629363	0.89[ASN][1000 genomes]
rs61708145	0.89[ASN][1000 genomes]
rs6439962	0.89[ASN][1000 genomes]
rs6439964	0.92[EUR][1000 genomes]
rs6439965	0.83[EUR][1000 genomes]
rs6439969	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67142314	0.88[EUR][1000 genomes]
rs6764740	0.91[EUR][1000 genomes]
rs6767867	0.91[EUR][1000 genomes]
rs6770562	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6772634	0.92[EUR][1000 genomes]
rs6773249	0.92[EUR][1000 genomes]
rs6785007	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785892	0.92[EUR][1000 genomes]
rs6788711	0.92[EUR][1000 genomes]
rs6789045	0.91[EUR][1000 genomes]
rs6789116	0.91[EUR][1000 genomes]
rs6789265	0.88[EUR][1000 genomes]
rs6797079	0.92[EUR][1000 genomes]
rs6809144	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6810200	0.89[ASN][1000 genomes]
rs713354	1.00[CEU][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72991046	1.00[ASN][1000 genomes]
rs7621150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626525	0.87[ASN][1000 genomes]
rs7627987	0.88[EUR][1000 genomes]
rs7631373	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7632043	0.87[ASN][1000 genomes]
rs7643287	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649116	0.88[ASN][1000 genomes]
rs7650179	0.88[EUR][1000 genomes]
rs7650190	0.88[EUR][1000 genomes]
rs7652381	1.00[CEU][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs765990	0.92[EUR][1000 genomes]
rs877142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957093	0.92[EUR][1000 genomes]
rs9833041	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9880468	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9880470	0.81[ASN][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	nsv591865	chr3:140396022-140728850	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140661800-140697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:140663400-140697400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:140664200-140703800	Weak transcription	Aorta	Aorta
4	chr3:140665400-140698400	Weak transcription	Brain Germinal Matrix	brain
5	chr3:140665800-140697600	Weak transcription	Gastric	stomach
6	chr3:140670000-140697200	Weak transcription	Esophagus	oesophagus
7	chr3:140670600-140698200	Weak transcription	Spleen	Spleen
8	chr3:140672200-140699000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:140672800-140698800	Weak transcription	Right Ventricle	heart
10	chr3:140672800-140700000	Weak transcription	Small Intestine	intestine
11	chr3:140673400-140698800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:140673400-140700200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:140673600-140699000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:140674400-140697200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:140675000-140697600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:140675200-140699000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:140675600-140698200	Weak transcription	Pancreas	Pancrea
18	chr3:140679800-140697200	Weak transcription	Brain Substantia Nigra	brain
19	chr3:140679800-140699000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:140679800-140699600	Weak transcription	Left Ventricle	heart
21	chr3:140680000-140697000	Weak transcription	Brain Angular Gyrus	brain
22	chr3:140680000-140697600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:140680000-140698600	Weak transcription	HSMMtube	muscle
24	chr3:140680000-140699200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:140680000-140699600	Weak transcription	NHEK	skin
26	chr3:140688800-140697000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:140690200-140697800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:140691600-140697600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:140692000-140697000	Strong transcription	Fetal Intestine Large	intestine
30	chr3:140692000-140697200	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:140692000-140697400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:140692000-140697400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:140692000-140697600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:140692000-140697800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:140692000-140699000	Strong transcription	HSMM	muscle
36	chr3:140692200-140697400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:140692200-140697400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:140692200-140697400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:140692200-140697600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:140692200-140697600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:140692200-140697600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr3:140692200-140698000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:140692400-140697200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:140692400-140697200	Strong transcription	Fetal Brain Female	brain
45	chr3:140692600-140697400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:140692600-140697400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:140692600-140697400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:140692600-140697400	Strong transcription	NH-A	brain
49	chr3:140692600-140698600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:140692800-140698200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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