Variant report

Variant	rs1610238
Chromosome Location	chr3:28280965-28280966
allele	A/G
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	TEAD4	chr3:28280603-28281001	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr3:28280518-28281049	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr3:28280614-28280967	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr3:28280570-28280967	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:28277439..28279511-chr3:28280296..28282426,2	MCF-7	breast:
2	chr3:28279814..28284603-chr3:28388127..28392296,9	K562	blood:
3	chr3:28270292..28273085-chr3:28279670..28282869,3	MCF-7	breast:
4	chr3:28279618..28281224-chr3:28281299..28282942,2	MCF-7	breast:
5	chr3:28279814..28285757-chr3:28388127..28392208,14	K562	blood:
6	chr3:28263497..28265020-chr3:28280684..28282522,2	K562	blood:
7	chr3:28279881..28282644-chr3:28339325..28342183,2	K562	blood:

No data

Variant related genes	Relation type
CMC1	TF binding region
ENSG00000163512	Chromatin interaction
ENSG00000206559	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11706332	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs11708424	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11720107	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs11918050	0.84[CHB][hapmap]
rs11921692	0.84[CHB][hapmap]
rs11921943	0.85[CHB][hapmap]
rs12107256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13081520	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs13082167	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs13083544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13085075	0.85[CHB][hapmap]
rs13085245	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13087143	1.00[ASW][hapmap];0.85[CHB][hapmap];0.89[MEX][hapmap]
rs13087774	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs13090296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090439	0.85[CHB][hapmap]
rs13092618	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13093242	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13095628	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs13095675	0.85[CHB][hapmap]
rs1599826	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1606386	0.92[CHB][hapmap]
rs1606388	0.92[CHB][hapmap];0.89[MEX][hapmap]
rs17021221	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17021306	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17021402	0.85[CHB][hapmap]
rs17357206	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs17638742	0.92[CHB][hapmap];0.89[MEX][hapmap]
rs17638991	0.85[CHB][hapmap];0.83[MEX][hapmap]
rs17695765	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs17695884	0.85[CHB][hapmap]
rs17696025	0.85[CHB][hapmap]
rs1870259	0.84[CHB][hapmap]
rs2016948	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34017994	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34419916	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34541614	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34681294	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34748842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35217335	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35232922	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35439056	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35460328	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35496780	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35530532	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35565264	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35575798	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35678778	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35768817	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35937120	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36105900	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs3762797	0.85[CHB][hapmap]
rs4452283	0.85[CHB][hapmap]
rs4680909	0.85[CHB][hapmap]
rs4680913	0.85[CHB][hapmap]
rs56946005	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66502736	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66716911	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67023418	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6771057	0.85[CHB][hapmap]
rs6771460	0.85[CHB][hapmap]
rs68097246	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7434193	0.83[CHB][hapmap]
rs7639750	0.85[CHB][hapmap]
rs7641491	0.85[CHB][hapmap]
rs7649498	0.85[CHB][hapmap]
rs7651883	0.85[CHB][hapmap]
rs9843464	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876648	chr3:28060456-28280965	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28273800-28281200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:28274200-28282000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:28277400-28282000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:28279000-28281800	Weak transcription	Primary T cells from cord blood	blood
5	chr3:28279200-28282000	Weak transcription	NHDF-Ad	bronchial
6	chr3:28279800-28281000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:28279800-28281400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:28279800-28281800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:28280000-28281000	Weak transcription	HepG2	liver
10	chr3:28280000-28282000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr3:28280000-28282200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:28280600-28281000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:28280600-28281000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:28280600-28281000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:28280600-28281200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:28280600-28281400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:28280600-28282000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:28280800-28281000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:28280800-28281000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:28280800-28281000	Enhancers	Psoas Muscle	Psoas
21	chr3:28280800-28281200	Enhancers	H9 Cell Line	embryonic stem cell
22	chr3:28280800-28281200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr3:28280800-28282200	Enhancers	HUES48 Cell Line	embryonic stem cell

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