Variant report

Variant	rs6730876
Chromosome Location	chr2:54827001-54827002
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54785770..54787299-chr2:54826149..54827905,2	K562	blood:
2	chr2:54822696..54824811-chr2:54826177..54828033,3	K562	blood:
3	chr2:54815022..54818519-chr2:54825874..54828742,4	K562	blood:
4	chr2:54822853..54825212-chr2:54825239..54827897,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10169439	1.00[CEU][hapmap]
rs10170355	1.00[CHB][hapmap]
rs10176359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10176445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10182836	1.00[CHB][hapmap]
rs10183043	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10183867	1.00[CHB][hapmap]
rs10184128	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs10188185	1.00[CHB][hapmap]
rs10188545	0.81[ASN][1000 genomes]
rs10193692	1.00[CHB][hapmap]
rs10205410	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10206143	1.00[CHB][hapmap]
rs10210502	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10528	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs1137645	1.00[CHB][hapmap]
rs11555856	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11892236	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11892443	1.00[CHB][hapmap]
rs11896957	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898032	0.82[ASN][1000 genomes]
rs11898033	0.82[ASN][1000 genomes]
rs11902659	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11902987	1.00[CHB][hapmap]
rs11904679	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs12713262	0.83[EUR][1000 genomes]
rs12713263	0.83[EUR][1000 genomes]
rs12713264	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12713265	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs12713268	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs12713269	1.00[CHB][hapmap]
rs12713270	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713271	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713272	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713273	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12987967	0.88[EUR][1000 genomes]
rs13004944	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13021606	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13021615	0.88[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs13386146	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13391522	1.00[CHB][hapmap]
rs13391803	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13399656	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13403284	1.00[CHB][hapmap]
rs13407214	0.81[ASN][1000 genomes]
rs13408295	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13428703	0.92[CEU][hapmap]
rs17039558	0.84[CEU][hapmap];0.89[CHB][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs17045939	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap]
rs17046036	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17046061	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17046067	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17046077	0.85[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs17046108	0.88[CHB][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs17046257	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs2048370	0.88[CHB][hapmap]
rs2229503	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2271329	0.88[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs3287	1.00[CHB][hapmap]
rs34077590	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34094680	0.89[EUR][1000 genomes]
rs34308676	0.85[EUR][1000 genomes]
rs34311770	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34978408	0.89[EUR][1000 genomes]
rs354232	0.89[CHB][hapmap]
rs35619551	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3739109	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs3796019	1.00[CHB][hapmap]
rs3796022	0.89[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4261758	0.84[CEU][hapmap];0.89[CHB][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4319969	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs4346422	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4347868	0.82[ASN][1000 genomes]
rs4358162	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374410	0.84[ASN][1000 genomes]
rs4455200	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4519566	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4577321	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57281248	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58419243	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61126015	0.85[EUR][1000 genomes]
rs6545430	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs6545435	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6545440	0.92[CEU][hapmap]
rs66693131	0.82[EUR][1000 genomes]
rs6706263	1.00[CHB][hapmap]
rs67079536	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6708082	0.92[CEU][hapmap]
rs6721612	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724136	0.84[EUR][1000 genomes]
rs67244067	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6734445	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6734536	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6739140	0.82[ASN][1000 genomes]
rs6740893	0.95[ASN][1000 genomes]
rs6741053	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6749802	0.82[ASN][1000 genomes]
rs6752720	0.92[CEU][hapmap]
rs6753004	0.92[CEU][hapmap]
rs72806653	0.83[EUR][1000 genomes]
rs7340302	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs7424459	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7556752	1.00[CHB][hapmap]
rs7564719	0.81[ASN][1000 genomes]
rs7569127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7582640	0.92[CEU][hapmap]
rs7584223	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7586066	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7599241	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7602992	0.83[EUR][1000 genomes]
rs7608414	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6730876	C2orf63	cis	cerebellum	SCAN
rs6730876	RPL23AP32	cis	cerebellum	SCAN
rs6730876	EML6	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:54816600-54828400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54822200-54827800	Genic enhancers	Fetal Muscle Leg	muscle
5	chr2:54822200-54828800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:54822200-54833800	Genic enhancers	HepG2	liver
7	chr2:54822400-54827600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:54822400-54827800	Enhancers	Colon Smooth Muscle	Colon
9	chr2:54822400-54833600	Enhancers	Psoas Muscle	Psoas
10	chr2:54822400-54833800	Enhancers	Stomach Mucosa	stomach
11	chr2:54822400-54834000	Enhancers	Right Atrium	heart
12	chr2:54822600-54827200	Enhancers	Brain Hippocampus Middle	brain
13	chr2:54822800-54831600	Genic enhancers	A549	lung
14	chr2:54823200-54831000	Genic enhancers	Fetal Intestine Large	intestine
15	chr2:54823400-54827200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:54823800-54829400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:54824000-54829400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:54824200-54827400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:54824200-54827400	Weak transcription	Fetal Kidney	kidney
20	chr2:54824200-54829600	Enhancers	Fetal Heart	heart
21	chr2:54824200-54830600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:54824200-54833600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:54824400-54828800	Enhancers	HMEC	breast
24	chr2:54824400-54829200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:54824600-54834400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:54824800-54829600	Genic enhancers	Primary hematopoietic stem cells	blood
27	chr2:54824800-54834400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:54824800-54839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:54825000-54829200	Genic enhancers	HSMM	muscle
30	chr2:54825000-54829800	Weak transcription	Fetal Brain Male	brain
31	chr2:54825200-54827600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:54825200-54828400	Strong transcription	GM12878-XiMat	blood
33	chr2:54825400-54827600	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr2:54825400-54827600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
35	chr2:54825400-54827800	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr2:54825400-54828200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:54825400-54828800	Strong transcription	Fetal Stomach	stomach
38	chr2:54825400-54829000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:54825600-54827200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr2:54825600-54827200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:54825600-54827200	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr2:54825600-54827600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:54825600-54827600	Genic enhancers	Brain Inferior Temporal Lobe	brain
44	chr2:54825600-54827600	Genic enhancers	Brain Substantia Nigra	brain
45	chr2:54825600-54827600	Enhancers	Esophagus	oesophagus
46	chr2:54825600-54827600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr2:54825600-54827600	Genic enhancers	HUVEC	blood vessel
48	chr2:54825600-54827800	Genic enhancers	Brain Anterior Caudate	brain
49	chr2:54825600-54827800	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr2:54825600-54828400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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