Variant report

Variant	rs9847842
Chromosome Location	chr3:160941129-160941130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:160941098-160941392	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:160941125-160941179	ProgFib	skin:	n/a	n/a
3	POLR2A	chr3:160940425-160941204	MCF-7	breast:	n/a	n/a
4	CHD1	chr3:160938248-160941179	IMR90	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
2	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
3	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
4	chr3:160472482..160474998-chr3:160940275..160941880,2	MCF-7	breast:
5	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:
6	chr3:160940674..160943053-chr3:161145134..161148083,2	MCF-7	breast:
7	chr3:160940058..160942666-chr3:161042036..161044035,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271052	TF binding region
NMD3	TF binding region
ENSG00000240138	Chromatin interaction
ENSG00000260572	Chromatin interaction
ENSG00000234851	Chromatin interaction
ENSG00000269888	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000163590	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1017799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12486069	0.87[ASN][1000 genomes]
rs12486111	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs12486998	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs12487002	0.89[JPT][hapmap]
rs12488127	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs12489004	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12489125	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12490149	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12494725	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12496235	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13315320	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13319558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13319771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1450518	0.88[JPT][hapmap]
rs16831799	0.85[AMR][1000 genomes]
rs16831850	1.00[GIH][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16831864	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16831882	0.87[ASN][1000 genomes]
rs16831942	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2306209	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28451189	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28704960	0.87[ASN][1000 genomes]
rs28713364	0.97[AMR][1000 genomes]
rs3925722	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4296611	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4352387	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4468992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4580574	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4635725	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57903480	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59567999	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59593286	0.83[AMR][1000 genomes]
rs59757775	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59776766	0.87[ASN][1000 genomes]
rs59867530	0.82[AMR][1000 genomes]
rs60121330	0.87[ASN][1000 genomes]
rs6441350	1.00[GIH][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6441363	0.94[AMR][1000 genomes]
rs6441365	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6441372	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6441375	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6762064	0.83[ASW][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6771581	0.83[AMR][1000 genomes]
rs6774919	0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6775446	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6775931	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6778186	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6782415	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6782518	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6785714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6787447	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6788738	0.97[AMR][1000 genomes]
rs6790805	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6794601	0.89[JPT][hapmap]
rs6796168	0.84[MEX][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6801664	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6805976	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73017340	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026933	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73026967	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026968	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026983	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026987	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026989	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73878309	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7615833	1.00[CHB][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7615868	0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7624791	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7626773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7634299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7651924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7652624	0.82[CHB][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9290070	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9290071	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9682249	0.85[AMR][1000 genomes]
rs9810351	0.87[ASN][1000 genomes]
rs9812574	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9818470	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9818835	0.87[ASN][1000 genomes]
rs9818992	0.82[ASN][1000 genomes]
rs9819793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9822705	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9822916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9823424	0.87[ASN][1000 genomes]
rs9824535	0.87[ASN][1000 genomes]
rs9824805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826857	1.00[GIH][hapmap];0.87[ASN][1000 genomes]
rs9830183	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9833270	1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9834806	0.94[AMR][1000 genomes]
rs9835530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9838945	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9841871	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9842290	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9850455	0.89[JPT][hapmap]
rs9851699	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9855112	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9855572	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9856742	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858907	0.87[ASN][1000 genomes]
rs9859641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9860980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9862867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9871753	1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9872514	0.89[JPT][hapmap]
rs9876077	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9877309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9884100	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9985364	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160938400-160941200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:160938400-160941400	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr3:160938400-160941600	Active TSS	Stomach Smooth Muscle	stomach
4	chr3:160938600-160941400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:160938600-160941400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:160938600-160941600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr3:160938600-160941600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:160938600-160941600	Active TSS	NHLF	lung
9	chr3:160938600-160942400	Active TSS	Right Ventricle	heart
10	chr3:160939600-160941200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr3:160939800-160941200	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr3:160939800-160941200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr3:160939800-160941200	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:160940000-160941400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr3:160940000-160941600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr3:160940000-160942400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr3:160940000-160971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:160940000-160977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:160940200-160941200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:160940200-160941200	Enhancers	Primary B cells from peripheral blood	blood
22	chr3:160940200-160941200	Enhancers	Primary T cells fromperipheralblood	blood
23	chr3:160940200-160941400	Flanking Active TSS	Dnd41	blood
24	chr3:160940200-160941600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr3:160940200-160941600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:160940200-160941800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr3:160940200-160942800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:160940200-160943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:160940200-160965400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:160940400-160941200	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr3:160940400-160941200	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr3:160940400-160941200	Flanking Active TSS	Fetal Lung	lung
33	chr3:160940400-160941200	Flanking Active TSS	Fetal Stomach	stomach
34	chr3:160940400-160941200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr3:160940400-160941200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr3:160940400-160941400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
37	chr3:160940400-160941400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:160940400-160941400	Flanking Active TSS	Hela-S3	cervix
39	chr3:160940400-160942000	Flanking Active TSS	HUVEC	blood vessel
40	chr3:160940400-160942200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:160940400-160943000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:160940600-160941200	Flanking Active TSS	Fetal Intestine Large	intestine
43	chr3:160940600-160941200	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr3:160940600-160941200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr3:160940600-160941200	Transcr. at gene 5' and 3'	HSMM	muscle
46	chr3:160940600-160941400	Flanking Active TSS	NHEK	skin
47	chr3:160940600-160941600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
48	chr3:160940600-160941800	Transcr. at gene 5' and 3'	A549	lung
49	chr3:160940600-160942200	Transcr. at gene 5' and 3'	K562	blood
50	chr3:160940800-160941200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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