Variant report

Variant	rs7207499
Chromosome Location	chr17:64447165-64447166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:64439765..64442544-chr17:64445195..64447511,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11869711	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17771145	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1860659	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34488708	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57178647	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58134548	1.00[ASN][1000 genomes]
rs59920126	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60283766	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62070448	1.00[ASN][1000 genomes]
rs62070449	1.00[ASN][1000 genomes]
rs62070451	1.00[ASN][1000 genomes]
rs62070454	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62070455	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62070456	0.92[ASN][1000 genomes]
rs8079085	0.86[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	nsv1061581	chr17:64389183-64477328	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1057876	chr17:64401469-64802341	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv543407	chr17:64401469-64802341	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1064970	chr17:64410784-64486268	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv457882	chr17:64410915-64471675	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv575896	chr17:64410915-64471675	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv457883	chr17:64410915-64510410	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv575897	chr17:64410915-64510410	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv457887	chr17:64410915-64518507	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv575898	chr17:64410915-64518507	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1062365	chr17:64411424-64482886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv543408	chr17:64411424-64482886	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv817351	chr17:64420296-64742555	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Post-traumatic stress disorder (asjusted for relatedness)	23726511	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7207499	LIMD2	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:64428400-64448400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:64429200-64463000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr17:64429600-64451800	Weak transcription	Osteobl	bone
4	chr17:64429600-64455600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr17:64430000-64452000	Weak transcription	Fetal Stomach	stomach
6	chr17:64436400-64462000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr17:64437600-64447800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr17:64437800-64450000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr17:64437800-64455200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr17:64438600-64456400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr17:64439000-64457600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr17:64439200-64459000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:64439800-64450000	Enhancers	Dnd41	blood
14	chr17:64440000-64447800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr17:64440400-64447800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr17:64441200-64457400	Weak transcription	K562	blood
17	chr17:64441400-64447800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:64441400-64454200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr17:64441800-64447600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr17:64441800-64453800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr17:64442400-64448800	Enhancers	HepG2	liver
22	chr17:64442600-64448400	Enhancers	Fetal Intestine Small	intestine
23	chr17:64442800-64455400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:64443000-64455200	Weak transcription	HSMM	muscle
25	chr17:64443200-64448200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr17:64443200-64448200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr17:64443800-64448000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr17:64444200-64448200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr17:64444200-64448800	Enhancers	Stomach Mucosa	stomach
30	chr17:64444400-64447600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr17:64444600-64450400	Weak transcription	Brain Anterior Caudate	brain
32	chr17:64444800-64447200	Weak transcription	Fetal Brain Female	brain
33	chr17:64444800-64447400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr17:64444800-64450800	Weak transcription	NH-A	brain
35	chr17:64444800-64455600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr17:64445000-64452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr17:64445200-64449600	Enhancers	Fetal Thymus	thymus
38	chr17:64445400-64450000	Weak transcription	Fetal Brain Male	brain
39	chr17:64445600-64448200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr17:64445600-64448200	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr17:64445600-64448800	Enhancers	A549	lung
42	chr17:64445800-64447200	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr17:64445800-64447200	Enhancers	Brain Hippocampus Middle	brain
44	chr17:64445800-64450200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr17:64445800-64450600	Weak transcription	Brain Germinal Matrix	brain
46	chr17:64445800-64455600	Weak transcription	Colon Smooth Muscle	Colon
47	chr17:64446000-64447800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:64446000-64448800	Enhancers	Primary T cells from cord blood	blood
49	chr17:64446200-64447200	Enhancers	Brain Angular Gyrus	brain
50	chr17:64446400-64447200	Enhancers	Brain Inferior Temporal Lobe	brain

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