Variant report

Variant	rs877142
Chromosome Location	chr3:140680962-140680963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:140678616-140684731	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:140658905..140661688-chr3:140680919..140682629,2	MCF-7	breast:
2	chr3:140670742..140673914-chr3:140680014..140683024,3	MCF-7	breast:
3	chr3:140680069..140681751-chr3:140681989..140683557,2	MCF-7	breast:
4	chr3:140676819..140681494-chr3:140682104..140687069,10	K562	blood:
5	chr3:140676819..140681121-chr3:140681142..140685749,7	K562	blood:

No data

Variant related genes	Relation type
SLC25A36	TF binding region
ENSG00000114120	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1047330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[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	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935414	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1109282	1.00[CHB][hapmap];0.81[JPT][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];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714438	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs11715248	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs11717620	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs11718040	1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs11718539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718563	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs11720342	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12489397	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]
rs13063450	0.90[EUR][1000 genomes]
rs13099706	0.90[EUR][1000 genomes]
rs1401509	0.87[AFR][1000 genomes]
rs1568337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1593623	0.87[AMR][1000 genomes];0.86[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];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs16851001	0.86[EUR][1000 genomes]
rs2042759	0.84[EUR][1000 genomes]
rs2081662	0.90[EUR][1000 genomes]
rs2292919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2310859	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2311491	0.90[EUR][1000 genomes]
rs2555702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871615	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs35140461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755764	1.00[CHB][hapmap];0.83[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];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs4068843	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4524250	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4528914	0.88[EUR][1000 genomes]
rs4538351	0.90[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	0.90[EUR][1000 genomes]
rs6439965	0.81[EUR][1000 genomes]
rs6439969	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67142314	0.86[EUR][1000 genomes]
rs6764740	0.88[EUR][1000 genomes]
rs6767867	0.88[EUR][1000 genomes]
rs6770562	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6772634	0.90[EUR][1000 genomes]
rs6773249	0.90[EUR][1000 genomes]
rs6785007	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785892	0.90[EUR][1000 genomes]
rs6788711	0.90[EUR][1000 genomes]
rs6789045	0.88[EUR][1000 genomes]
rs6789116	0.88[EUR][1000 genomes]
rs6789265	0.86[EUR][1000 genomes]
rs6797079	0.90[EUR][1000 genomes]
rs6809144	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6810200	0.89[ASN][1000 genomes]
rs713354	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[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];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626525	0.87[ASN][1000 genomes]
rs7627987	0.86[EUR][1000 genomes]
rs7631373	0.80[AMR][1000 genomes];0.86[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];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649116	0.88[ASN][1000 genomes]
rs7650179	0.86[EUR][1000 genomes]
rs7650190	0.86[EUR][1000 genomes]
rs7652381	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs765990	0.90[EUR][1000 genomes]
rs957093	0.90[EUR][1000 genomes]
rs9833041	0.82[AMR][1000 genomes];0.86[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:4 , 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
2	nsv1005522	chr3:140454632-140685915	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536732	chr3:140454632-140685915	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv1793115	chr3:140663107-140693053	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 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	chr3:140662200-140696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:140662400-140692200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:140662600-140696800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:140662800-140682200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:140662800-140695800	Weak transcription	NHLF	lung
7	chr3:140663000-140681600	Weak transcription	NH-A	brain
8	chr3:140663200-140692600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:140663200-140696000	Weak transcription	Fetal Stomach	stomach
10	chr3:140663400-140697400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:140663600-140692600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:140664200-140692400	Weak transcription	Fetal Brain Female	brain
13	chr3:140664200-140703800	Weak transcription	Aorta	Aorta
14	chr3:140665400-140698400	Weak transcription	Brain Germinal Matrix	brain
15	chr3:140665800-140697600	Weak transcription	Gastric	stomach
16	chr3:140670000-140692600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:140670000-140693800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:140670000-140697200	Weak transcription	Esophagus	oesophagus
19	chr3:140670600-140698200	Weak transcription	Spleen	Spleen
20	chr3:140670800-140696800	Weak transcription	Lung	lung
21	chr3:140671400-140694000	Weak transcription	Ovary	ovary
22	chr3:140672000-140694800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:140672200-140692000	Weak transcription	HUVEC	blood vessel
24	chr3:140672200-140699000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:140672600-140694200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:140672600-140695000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:140672800-140692800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:140672800-140698800	Weak transcription	Right Ventricle	heart
29	chr3:140672800-140700000	Weak transcription	Small Intestine	intestine
30	chr3:140673200-140694200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:140673400-140692800	Weak transcription	Brain Anterior Caudate	brain
32	chr3:140673400-140693400	Weak transcription	Fetal Intestine Small	intestine
33	chr3:140673400-140694000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:140673400-140698800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:140673400-140700200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:140673600-140683800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:140673600-140699000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:140673800-140694000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:140674400-140697200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:140674600-140687000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:140674800-140685000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:140674800-140692600	Weak transcription	Psoas Muscle	Psoas
43	chr3:140675000-140697600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:140675200-140695200	Weak transcription	Fetal Brain Male	brain
45	chr3:140675200-140699000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:140675400-140684000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:140675400-140690600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:140675400-140690800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:140675600-140692600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:140675600-140698200	Weak transcription	Pancreas	Pancrea

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