Variant report

Variant	rs6712029
Chromosome Location	chr2:48557930-48557931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48550065..48552046-chr2:48557575..48559707,2	MCF-7	breast:
2	chr2:48541299..48543894-chr2:48556548..48558555,2	MCF-7	breast:
3	chr2:48552083..48554152-chr2:48555088..48558115,3	K562	blood:
4	chr2:48545774..48548252-chr2:48556563..48558332,2	K562	blood:

Variant related genes	Relation type
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10153773	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10174717	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10180295	0.90[ASN][1000 genomes]
rs10186237	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10193072	0.90[ASN][1000 genomes]
rs10199431	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10208124	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10454133	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs10495951	0.91[JPT][hapmap]
rs10495952	0.91[JPT][hapmap]
rs11676168	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11679523	0.91[JPT][hapmap]
rs11680916	0.95[JPT][hapmap]
rs11682044	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11682633	0.81[ASN][1000 genomes]
rs11682931	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11685861	0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11688481	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11690690	0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11690748	0.91[JPT][hapmap]
rs11690845	0.91[JPT][hapmap]
rs12616792	0.81[ASN][1000 genomes]
rs12713008	0.82[ASN][1000 genomes]
rs12713009	0.80[ASN][1000 genomes]
rs13003076	0.82[ASN][1000 genomes]
rs13383364	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13385535	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13386751	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13387171	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13388291	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13392004	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13426834	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13432998	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17037289	0.91[JPT][hapmap]
rs17037298	0.91[JPT][hapmap]
rs17855177	0.91[JPT][hapmap]
rs2471405	0.82[ASN][1000 genomes]
rs28806843	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28841370	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4267555	0.80[CEU][hapmap]
rs4290706	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4344965	0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4411759	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4547573	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4641990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56163539	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56352447	0.99[ASN][1000 genomes]
rs57668696	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58660534	0.94[ASN][1000 genomes]
rs59264464	0.94[ASN][1000 genomes]
rs59412192	0.94[ASN][1000 genomes]
rs59761994	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60677957	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62136987	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62137001	0.94[ASN][1000 genomes]
rs62137002	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62137003	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62137005	0.94[ASN][1000 genomes]
rs62137006	0.94[ASN][1000 genomes]
rs62137007	0.94[ASN][1000 genomes]
rs62137008	0.91[ASN][1000 genomes]
rs62137009	0.91[ASN][1000 genomes]
rs62137015	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62138801	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545026	0.92[YRI][hapmap]
rs6545027	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545028	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545029	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545034	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545035	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545036	0.88[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6705802	0.91[JPT][hapmap];0.85[LWK][hapmap];0.88[YRI][hapmap]
rs6718068	0.91[JPT][hapmap]
rs6743757	0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6749773	0.87[AMR][1000 genomes]
rs6757206	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72818493	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72820403	0.80[ASN][1000 genomes]
rs72820405	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72887649	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7340322	0.82[ASN][1000 genomes]
rs7562069	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7562816	0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7566239	0.91[JPT][hapmap];0.96[YRI][hapmap]
rs7568960	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7574125	0.86[ASN][1000 genomes]
rs7576964	0.81[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap]
rs7577237	0.91[JPT][hapmap];0.96[YRI][hapmap]
rs7579932	0.92[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7600794	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7606104	0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9309152	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer 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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48543400-48568600	Weak transcription	HSMM	muscle
2	chr2:48543600-48559400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:48543600-48561000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:48543600-48570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:48544200-48559600	Weak transcription	Fetal Kidney	kidney
6	chr2:48544400-48558600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:48544400-48570400	Weak transcription	NHEK	skin
8	chr2:48544400-48570800	Weak transcription	HMEC	breast
9	chr2:48544600-48558600	Weak transcription	Spleen	Spleen
10	chr2:48544600-48564400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:48544800-48559400	Weak transcription	Right Atrium	heart
12	chr2:48548600-48570600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:48550400-48562200	Enhancers	Brain Substantia Nigra	brain
14	chr2:48550600-48559400	Enhancers	Brain Hippocampus Middle	brain
15	chr2:48551600-48558600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:48552000-48558800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:48552400-48561000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr2:48552400-48561600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:48552400-48566200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:48552400-48570600	Weak transcription	Aorta	Aorta
21	chr2:48553400-48558600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:48553400-48574400	Weak transcription	Lung	lung
23	chr2:48553800-48570800	Weak transcription	Thymus	Thymus
24	chr2:48554400-48558200	Enhancers	A549	lung
25	chr2:48554400-48561000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr2:48554400-48570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:48554800-48561600	Weak transcription	Psoas Muscle	Psoas
28	chr2:48554800-48562000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:48555000-48560400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:48555000-48560400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr2:48555000-48561600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr2:48555000-48562000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr2:48555200-48558200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr2:48555200-48558200	Enhancers	HepG2	liver
35	chr2:48555200-48559000	Enhancers	Brain Cingulate Gyrus	brain
36	chr2:48555200-48560800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr2:48555400-48558000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr2:48555400-48558200	Enhancers	Liver	Liver
39	chr2:48555400-48558400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:48555400-48558800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:48555400-48558800	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr2:48555400-48570600	Weak transcription	NHLF	lung
43	chr2:48555800-48558000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr2:48556000-48558200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr2:48556000-48560400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr2:48556800-48558200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:48556800-48558600	Weak transcription	Small Intestine	intestine
48	chr2:48556800-48558600	Weak transcription	NHDF-Ad	bronchial
49	chr2:48556800-48558800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:48556800-48559600	Weak transcription	HSMMtube	muscle

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