Variant report

Variant	rs1257010
Chromosome Location	chr2:97633814-97633815
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97631877..97635109-chr2:97650329..97653813,3	MCF-7	breast:
2	chr2:97533874..97536783-chr2:97631835..97634576,3	MCF-7	breast:
3	chr2:97632347..97633971-chr2:97643638..97646130,2	MCF-7	breast:
4	chr2:97623724..97626251-chr2:97633605..97636499,4	K562	blood:

Variant related genes	Relation type
ENSG00000168754	Chromatin interaction
ENSG00000168758	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11164113	0.80[CHB][hapmap]
rs1148592	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs1148595	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs11688134	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11688903	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1257006	1.00[JPT][hapmap]
rs1257013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1257014	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1257021	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1257022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1257026	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1257084	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1257089	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1257101	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1257117	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12995874	0.89[ASN][1000 genomes]
rs1669760	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1796025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1796043	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1796048	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796050	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2443873	0.93[JPT][hapmap]
rs2463904	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4063952	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6730782	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7569432	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs9324210	0.81[AMR][1000 genomes];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	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv1001432	chr2:97591069-97671395	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	esv32727	chr2:97616488-97643975	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1257010	UNQ2430	cis	multi-tissue	Pritchard
rs1257010	ANKRD36B	cis	Thyroid	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97620800-97643600	Weak transcription	Right Atrium	heart
2	chr2:97625600-97634200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr2:97626200-97635800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:97629200-97634200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:97630600-97635600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:97630600-97635600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:97630600-97635600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:97630600-97635800	Weak transcription	Colonic Mucosa	Colon
9	chr2:97630600-97635800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:97630600-97636000	Weak transcription	Fetal Intestine Small	intestine
11	chr2:97630800-97635600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:97630800-97636200	Weak transcription	Fetal Intestine Large	intestine
13	chr2:97631200-97635400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:97631600-97635800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:97631800-97637000	Enhancers	Brain Substantia Nigra	brain
16	chr2:97631800-97637400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr2:97632000-97636600	Enhancers	Brain Anterior Caudate	brain
18	chr2:97632200-97634600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:97632200-97635200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:97632200-97636400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:97632200-97636800	Enhancers	Brain Cingulate Gyrus	brain
22	chr2:97632400-97636400	Enhancers	Brain Angular Gyrus	brain
23	chr2:97633000-97634000	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:97633000-97635400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:97633200-97635600	Weak transcription	Primary T cells from cord blood	blood
26	chr2:97633200-97635800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:97633200-97643200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:97633400-97635800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:97633400-97635800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:97633400-97635800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:97633600-97635400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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