Variant report

Variant	rs11258536
Chromosome Location	chr10:6447553-6447554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6240172..6247565-chr10:6441706..6450964,34	MCF-7	breast:
2	chr10:6407311..6409448-chr10:6446152..6447736,2	MCF-7	breast:
3	chr10:6447268..6450081-chr10:6450323..6453408,3	K562	blood:
4	chr10:6241662..6248347-chr10:6438932..6450669,77	MCF-7	breast:
5	chr10:6184712..6187301-chr10:6446699..6448973,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10906464	1.00[JPT][hapmap]
rs10906468	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10906490	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11258563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11258586	0.83[AFR][1000 genomes]
rs11258608	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11258610	0.86[EUR][1000 genomes]
rs11258759	0.80[CEU][hapmap]
rs11258802	0.83[AFR][1000 genomes]
rs12146312	0.83[GIH][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap]
rs12355507	0.83[AFR][1000 genomes]
rs12358161	1.00[LWK][hapmap];0.83[AFR][1000 genomes]
rs2453	0.88[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap]
rs4750439	0.80[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap]
rs4750495	0.83[GIH][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap]
rs586457	0.84[TSI][hapmap]
rs604856	0.81[AMR][1000 genomes]
rs616490	0.89[EUR][1000 genomes]
rs670804	0.84[TSI][hapmap]
rs673964	0.84[TSI][hapmap]
rs677986	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs7091849	0.86[EUR][1000 genomes]
rs7095942	1.00[LWK][hapmap];0.83[AFR][1000 genomes]
rs7096751	1.00[LWK][hapmap]
rs7099451	0.83[GIH][hapmap]
rs72781706	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs944713	0.80[CEU][hapmap]
rs944715	0.88[GIH][hapmap];0.94[TSI][hapmap]

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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv3357360	chr10:6447346-6451644	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11258536	ANKRD16	cis	parietal	SCAN
rs11258536	CALML5	cis	brain	BrainEAC
rs11258536	AKR1CL1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6433800-6448600	Weak transcription	Primary T cells from cord blood	blood
2	chr10:6443400-6452000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:6443800-6451800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr10:6444000-6447600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr10:6444000-6447600	Weak transcription	Pancreas	Pancrea
6	chr10:6444000-6447800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr10:6444000-6448200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr10:6444000-6448200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr10:6444000-6451200	Weak transcription	Aorta	Aorta
10	chr10:6444000-6451400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr10:6444000-6451600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr10:6444000-6452000	Weak transcription	Brain Anterior Caudate	brain
13	chr10:6444000-6452000	Weak transcription	Right Ventricle	heart
14	chr10:6444000-6452400	Weak transcription	Right Atrium	heart
15	chr10:6444200-6448000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:6444200-6448200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr10:6444200-6452000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr10:6445200-6449000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:6445200-6451000	Weak transcription	Dnd41	blood
20	chr10:6445600-6450800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:6445600-6452000	Weak transcription	Psoas Muscle	Psoas
22	chr10:6445800-6448600	Weak transcription	Thymus	Thymus
23	chr10:6446000-6448600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:6446000-6452000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr10:6446400-6447800	Weak transcription	A549	lung
26	chr10:6447200-6447600	Active TSS	Spleen	Spleen
27	chr10:6447400-6448600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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