Variant report

Variant	rs1258042
Chromosome Location	chr1:47015073-47015074
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46999948..47005205-chr1:47009363..47015200,7	K562	blood:
2	chr1:47012476..47015757-chr1:47016043..47020828,4	K562	blood:
3	chr1:47012476..47015680-chr1:47016269..47019098,3	K562	blood:

Variant related genes	Relation type
ENSG00000269956	Chromatin interaction
ENSG00000162456	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11211298	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1258022	1.00[GIH][hapmap]
rs1258028	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1258040	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1258046	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320556	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13373780	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17102252	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2486164	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2486165	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59291308	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60242607	1.00[EUR][1000 genomes]
rs60309634	1.00[EUR][1000 genomes]
rs60791879	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61011128	1.00[EUR][1000 genomes]
rs61629467	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61691256	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6660663	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs72894674	1.00[EUR][1000 genomes]
rs7515750	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7525300	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs942253	1.00[EUR][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	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS 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 miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv998422	chr1:46969626-47023671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv534953	chr1:46969626-47023671	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1009899	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv534954	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46999600-47035000	Weak transcription	Right Atrium	heart
2	chr1:47012400-47015200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:47013800-47022000	Weak transcription	HMEC	breast
4	chr1:47014000-47015200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:47014000-47015400	Weak transcription	Esophagus	oesophagus
6	chr1:47014000-47015400	Weak transcription	K562	blood
7	chr1:47014000-47026600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:47014200-47015200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:47014200-47016800	Enhancers	Fetal Brain Male	brain
10	chr1:47014400-47016800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:47014800-47015400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:47014800-47015400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr1:47015000-47015200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
14	chr1:47015000-47015200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
15	chr1:47015000-47015200	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr1:47015000-47015200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
17	chr1:47015000-47015200	Enhancers	Fetal Brain Female	brain
18	chr1:47015000-47015400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:47015000-47015400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
20	chr1:47015000-47015400	Enhancers	Fetal Muscle Leg	muscle
21	chr1:47015000-47015600	Enhancers	Colon Smooth Muscle	Colon
22	chr1:47015000-47015800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:47015000-47015800	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:47015000-47015800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
25	chr1:47015000-47016000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:47015000-47016000	Enhancers	Primary T cells fromperipheralblood	blood
27	chr1:47015000-47016000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:47015000-47016000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:47015000-47016400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:47015000-47016600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:47015000-47016600	Enhancers	Brain Germinal Matrix	brain
32	chr1:47015000-47016800	Bivalent Enhancer	Fetal Stomach	stomach
33	chr1:47015000-47019000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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