Variant report

Variant	rs6434128
Chromosome Location	chr2:153479857-153479858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:153479609-153479897	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:153479840-153479888	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153031094..153033506-chr2:153477757..153480086,2	K562	blood:
2	chr2:153474747..153476938-chr2:153478477..153480006,2	MCF-7	breast:

Variant related genes	Relation type
FMNL2	TF binding region
ENSG00000157827	Chromatin interaction
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10172024	0.90[CHB][hapmap]
rs1036526	0.95[CHB][hapmap]
rs1065266	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs10931229	0.95[CHB][hapmap]
rs1128804	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs11899051	0.94[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs12477881	0.90[CHB][hapmap]
rs12621561	0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs12693415	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13010731	0.90[CHB][hapmap]
rs13031469	0.95[CHB][hapmap]
rs13417781	0.81[CHB][hapmap]
rs13419068	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1370498	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs1437678	0.95[CHB][hapmap]
rs16831548	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs16831740	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs17328734	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs17400645	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.83[ASN][1000 genomes]
rs1962313	0.85[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs1986743	0.85[CHB][hapmap];0.89[CHD][hapmap]
rs1992146	0.95[CHB][hapmap]
rs2118377	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs2304556	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs2346539	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2346540	0.85[ASN][1000 genomes]
rs2346542	0.90[CHB][hapmap]
rs2346543	0.80[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2346549	0.81[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs2346550	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs3171980	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs3175	0.89[CHD][hapmap]
rs3748937	0.83[ASN][1000 genomes]
rs3748938	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs3748939	0.90[CHB][hapmap]
rs3762503	0.80[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[ASN][1000 genomes]
rs3762507	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs4233660	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs4267470	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs4664121	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs4664122	0.95[CHB][hapmap]
rs4664601	0.80[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[ASN][1000 genomes]
rs4664604	0.90[CHB][hapmap]
rs4664605	0.85[CHB][hapmap];0.94[CHD][hapmap];0.82[ASN][1000 genomes]
rs4664606	0.85[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs4664607	0.90[CHB][hapmap]
rs4664609	0.82[ASN][1000 genomes]
rs4664610	0.85[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs6434161	0.90[CHB][hapmap]
rs6434162	0.90[CHB][hapmap]
rs6727279	0.84[ASN][1000 genomes]
rs6744923	0.80[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs6746079	0.85[ASN][1000 genomes]
rs6748160	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs72871191	0.85[ASN][1000 genomes]
rs72872607	0.85[ASN][1000 genomes]
rs7556673	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs7558920	0.80[ASN][1000 genomes]
rs7560393	0.90[CHB][hapmap]
rs7576847	0.83[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7582253	0.90[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7589899	0.86[CHD][hapmap]
rs7593347	0.94[CHB][hapmap]
rs7596408	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7599946	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs7608603	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs9288121	0.95[CHB][hapmap]
rs9288125	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs9789505	0.85[ASN][1000 genomes]
rs9789521	0.84[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.83[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	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6434128	NR4A2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153454800-153496600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:153457200-153505000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:153463800-153502800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:153464000-153502800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:153464600-153480000	Strong transcription	NHEK	skin
6	chr2:153467200-153504000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:153468000-153480000	Strong transcription	HepG2	liver
8	chr2:153468000-153483200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:153468600-153480400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:153468600-153495800	Weak transcription	Esophagus	oesophagus
11	chr2:153468800-153492000	Weak transcription	Liver	Liver
12	chr2:153469000-153493800	Weak transcription	Spleen	Spleen
13	chr2:153469000-153496400	Weak transcription	Colonic Mucosa	Colon
14	chr2:153469000-153509800	Weak transcription	Small Intestine	intestine
15	chr2:153469200-153481200	Weak transcription	Right Atrium	heart
16	chr2:153469200-153484400	Weak transcription	Psoas Muscle	Psoas
17	chr2:153469200-153495200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:153469600-153487200	Weak transcription	Fetal Thymus	thymus
19	chr2:153469600-153496800	Weak transcription	HSMM	muscle
20	chr2:153470400-153483600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:153470600-153480400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:153470600-153483400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:153471000-153507000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:153471400-153482800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:153471600-153482200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:153472000-153522000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:153472800-153480000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:153473000-153500600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:153473200-153480000	Strong transcription	Fetal Intestine Large	intestine
30	chr2:153473800-153496400	Weak transcription	Osteobl	bone
31	chr2:153474400-153481400	Weak transcription	A549	lung
32	chr2:153474400-153486200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:153474400-153505000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr2:153474800-153484800	Weak transcription	Ovary	ovary
35	chr2:153475200-153480200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:153475200-153482000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:153475400-153480200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:153475800-153493000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:153476600-153492800	Weak transcription	Gastric	stomach
40	chr2:153477000-153484200	Weak transcription	Hela-S3	cervix
41	chr2:153477200-153483200	Weak transcription	Fetal Kidney	kidney
42	chr2:153477200-153484800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr2:153477600-153489800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:153477800-153480600	Strong transcription	Fetal Stomach	stomach
45	chr2:153477800-153481000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:153477800-153483000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:153477800-153483200	Weak transcription	NHDF-Ad	bronchial
48	chr2:153477800-153486200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:153477800-153488000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:153477800-153488200	Weak transcription	Pancreas	Pancrea

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