Variant report

Variant	rs17743946
Chromosome Location	chr11:85392873-85392874
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85373957..85377643-chr11:85392159..85394287,3	K562	blood:
2	chr11:85373910..85377412-chr11:85390875..85393447,4	MCF-7	breast:
3	chr11:85374551..85377717-chr11:85388541..85395552,6	MCF-7	breast:
4	chr11:85392237..85393792-chr11:85395923..85397928,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC89-1	chr11:85389665-85393535	NONHSAT023443

Variant related genes	Relation type
ENSG00000179071	Chromatin interaction
ENSG00000137504	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11826218	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1445498	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1445500	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1445501	1.00[JPT][hapmap]
rs1445505	1.00[JPT][hapmap]
rs1445511	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17817230	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17817254	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2044390	1.00[JPT][hapmap]
rs55945805	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102361	1.00[JPT][hapmap]
rs7116742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7121363	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7127477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931771	1.00[JPT][hapmap]
rs7943104	1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv898048	chr11:85206156-85404138	Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17743946	CCDC83	cis	parietal	SCAN
rs17743946	ME3	cis	cerebellum	SCAN
rs17743946	FZD4	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85389000-85393200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr11:85390600-85393200	Weak transcription	Fetal Brain Male	brain
3	chr11:85391200-85393200	Weak transcription	Primary B cells from cord blood	blood
4	chr11:85391800-85393000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr11:85391800-85393200	Enhancers	Fetal Thymus	thymus
6	chr11:85391800-85393400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:85392000-85393000	Enhancers	Brain Angular Gyrus	brain
8	chr11:85392200-85393000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr11:85392200-85393200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr11:85392200-85393200	Weak transcription	Right Ventricle	heart
11	chr11:85392200-85393400	Weak transcription	Right Atrium	heart
12	chr11:85392200-85393400	Enhancers	Stomach Smooth Muscle	stomach
13	chr11:85392400-85393400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:85392400-85393400	Weak transcription	Small Intestine	intestine
15	chr11:85392400-85396200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:85392400-85396200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:85392600-85393000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:85392600-85393000	Enhancers	Fetal Kidney	kidney
19	chr11:85392600-85393000	Weak transcription	Ovary	ovary
20	chr11:85392600-85393000	Enhancers	A549	lung
21	chr11:85392600-85393200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr11:85392600-85393200	Enhancers	Fetal Heart	heart
23	chr11:85392800-85393000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:85392800-85393000	Enhancers	Brain Germinal Matrix	brain
25	chr11:85392800-85393200	Enhancers	Primary hematopoietic stem cells	blood
26	chr11:85392800-85393200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:85392800-85393200	Enhancers	Brain Hippocampus Middle	brain
28	chr11:85392800-85393200	Enhancers	Brain Substantia Nigra	brain
29	chr11:85392800-85393200	Enhancers	Colon Smooth Muscle	Colon
30	chr11:85392800-85393200	Enhancers	GM12878-XiMat	blood
31	chr11:85392800-85393400	Enhancers	Stomach Mucosa	stomach
32	chr11:85392800-85393600	Flanking Active TSS	Fetal Lung	lung

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