Variant report

Variant	rs73050254
Chromosome Location	chr7:3129614-3129615
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	CTCF	chr7:3128912-3129696	A549	lung:	n/a	chr7:3129314-3129323 chr7:3129415-3129423 chr7:3129243-3129252
2	CTCF	chr7:3129580-3129730	RPTEC	kidney:	n/a	n/a
3	SMC3	chr7:3128994-3129783	SK-N-SH	brain:	n/a	chr7:3129016-3129030
4	RAD21	chr7:3128685-3129786	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr7:3128924-3129705	SK-N-SH	brain:	n/a	chr7:3129314-3129323 chr7:3129415-3129423 chr7:3129243-3129252
6	CTCF	chr7:3129520-3129670	GM12865	blood:	n/a	n/a
7	RAD21	chr7:3129177-3129625	HCT-116	colon:	n/a	n/a
8	CTCF	chr7:3129009-3129635	MCF-7	breast:	n/a	chr7:3129314-3129323 chr7:3129415-3129423 chr7:3129243-3129252

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3128837..3129871-chr7:3239803..3240577,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228334	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1011189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499320	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951041	0.89[ASN][1000 genomes]
rs11772425	0.89[ASN][1000 genomes]
rs11983132	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12700543	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17239772	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722398	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6949212	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6965655	0.89[ASN][1000 genomes]
rs6967398	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6968867	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6971695	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73033516	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73044327	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73050253	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73050272	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73050273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73050289	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs747248	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7792757	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7793674	0.96[EUR][1000 genomes]
rs7801254	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7802299	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7805429	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809283	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7811825	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8180717	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022938	chr7:2899514-3131881	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv605873	chr7:2920067-3204177	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1026476	chr7:2965034-3311344	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv538656	chr7:2965034-3311344	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv464260	chr7:2966138-3315572	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv605874	chr7:2966138-3315572	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1018287	chr7:2967524-3298539	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv538657	chr7:2967524-3298539	Bivalent/Poised TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv887319	chr7:3099853-3134593	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv887320	chr7:3110446-3134593	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv605875	chr7:3117801-3134593	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1020680	chr7:3125512-3204521	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1027945	chr7:3125512-3208071	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3123000-3130200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr7:3126800-3131000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:3128800-3131400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr7:3128800-3131600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:3128800-3131600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr7:3128800-3132200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr7:3128800-3134200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr7:3128800-3134400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:3129000-3131200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr7:3129000-3131800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr7:3129000-3131800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr7:3129200-3130600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:3129200-3131800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr7:3129400-3129800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr7:3129400-3131400	Enhancers	Primary T cells from cord blood	blood
16	chr7:3129400-3134200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:3129600-3130600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:3129600-3131200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:3129600-3132000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr7:3129600-3134600	Enhancers	Fetal Thymus	thymus

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