Variant report

Variant	rs17035323
Chromosome Location	chr4:106091978-106091979
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	chr4:106067292..106069656-chr4:106090639..106093477,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1391436	1.00[ASN][1000 genomes]
rs17035436	1.00[ASN][1000 genomes]
rs17035475	0.89[MEX][hapmap]
rs1986799	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1986800	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4560414	1.00[ASN][1000 genomes]
rs4698934	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698935	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4699160	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67776122	0.91[EUR][1000 genomes]
rs72665913	0.93[EUR][1000 genomes]
rs72665914	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72665916	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72665920	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72665924	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665926	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665928	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665931	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665935	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655049	1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17035323	THNSL1	trans	parietal	SCAN
rs17035323	BANK1	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106069400-106114200	Weak transcription	Esophagus	oesophagus
2	chr4:106069600-106102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:106069800-106101000	Weak transcription	HSMM	muscle
4	chr4:106069800-106101800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:106070400-106107800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:106070400-106111600	Weak transcription	Placenta	Placenta
7	chr4:106071000-106100800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:106072600-106100600	Weak transcription	Adipose Nuclei	Adipose
9	chr4:106076200-106092800	Weak transcription	Psoas Muscle	Psoas
10	chr4:106076200-106093000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:106077000-106100800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:106077000-106112000	Weak transcription	Aorta	Aorta
13	chr4:106078000-106092200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:106078000-106112800	Weak transcription	Fetal Kidney	kidney
15	chr4:106080600-106101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:106080600-106102800	Weak transcription	NHEK	skin
17	chr4:106080600-106105800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:106080600-106107800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:106080800-106095200	Weak transcription	Fetal Intestine Large	intestine
20	chr4:106083600-106097200	ZNF genes & repeats	GM12878-XiMat	blood
21	chr4:106083600-106100800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:106083600-106100800	Weak transcription	Right Ventricle	heart
23	chr4:106083600-106109200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:106083800-106092800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:106083800-106092800	Weak transcription	Brain Anterior Caudate	brain
26	chr4:106083800-106095600	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:106083800-106095800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:106083800-106100400	Weak transcription	Stomach Mucosa	stomach
29	chr4:106083800-106104800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:106083800-106111400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:106084000-106105000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:106084600-106092800	Weak transcription	K562	blood
33	chr4:106084800-106127400	Weak transcription	Brain Germinal Matrix	brain
34	chr4:106085200-106093600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:106085600-106112800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:106085800-106093000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:106086000-106105600	Weak transcription	Fetal Lung	lung
38	chr4:106088600-106092000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:106089600-106100800	Weak transcription	Small Intestine	intestine
40	chr4:106090000-106092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:106090000-106095400	Weak transcription	Fetal Intestine Small	intestine
42	chr4:106090400-106105600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:106090600-106094000	Enhancers	HepG2	liver
44	chr4:106090600-106107000	Weak transcription	NH-A	brain
45	chr4:106091000-106092800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr4:106091200-106092400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:106091400-106092000	Enhancers	Primary B cells from peripheral blood	blood
48	chr4:106091400-106092600	Strong transcription	Primary B cells from cord blood	blood
49	chr4:106091400-106092600	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr4:106091400-106093000	Enhancers	Primary neutrophils fromperipheralblood	blood

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