Variant report

Variant	rs17397408
Chromosome Location	chr2:33333871-33333872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:33332965..33336318-chr2:33345461..33348526,4	K562	blood:
2	chr2:33333082..33335535-chr2:33335888..33338274,2	K562	blood:
3	chr2:33323744..33329444-chr2:33330202..33334725,9	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10490453	1.00[ASN][1000 genomes]
rs17325656	1.00[ASN][1000 genomes]
rs17396752	1.00[ASN][1000 genomes]
rs17396759	1.00[ASN][1000 genomes]
rs219030	1.00[ASN][1000 genomes]
rs219140	1.00[ASN][1000 genomes]
rs219141	1.00[ASN][1000 genomes]
rs219143	1.00[ASN][1000 genomes]
rs219148	1.00[ASN][1000 genomes]
rs219149	1.00[ASN][1000 genomes]
rs219150	1.00[ASN][1000 genomes]
rs219153	1.00[ASN][1000 genomes]
rs219154	1.00[ASN][1000 genomes]
rs219156	1.00[ASN][1000 genomes]
rs219157	1.00[ASN][1000 genomes]
rs219158	1.00[ASN][1000 genomes]
rs219159	1.00[ASN][1000 genomes]
rs219160	1.00[ASN][1000 genomes]
rs219161	1.00[ASN][1000 genomes]
rs219165	1.00[ASN][1000 genomes]
rs219169	1.00[ASN][1000 genomes]
rs219173	1.00[ASN][1000 genomes]
rs34659319	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34924458	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35316632	1.00[ASN][1000 genomes]
rs35434665	1.00[ASN][1000 genomes]
rs67128703	1.00[AFR][1000 genomes]
rs72791775	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869582	chr2:32626571-33335810	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1012897	chr2:32635272-33335508	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1012472	chr2:32657052-33338578	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005878	chr2:32724734-33335870	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv535620	chr2:32724734-33335870	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
9	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1001408	chr2:33248877-33341137	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv535625	chr2:33248877-33341137	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	esv33628	chr2:33257484-33455355	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv1012946	chr2:33294522-33370391	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv535626	chr2:33294522-33370391	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv873789	chr2:33297967-33390188	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17397408	FAM98A	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33328600-33334000	Weak transcription	Fetal Kidney	kidney
2	chr2:33328800-33347800	Weak transcription	Psoas Muscle	Psoas
3	chr2:33329600-33335600	Weak transcription	Liver	Liver
4	chr2:33330000-33335600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:33330000-33337200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:33330400-33335600	Weak transcription	A549	lung
7	chr2:33331400-33334600	Enhancers	Fetal Heart	heart
8	chr2:33332400-33334400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:33332600-33334400	Enhancers	Osteobl	bone
10	chr2:33332600-33334600	Enhancers	NH-A	brain
11	chr2:33332800-33334600	Enhancers	NHLF	lung
12	chr2:33332800-33335000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:33333000-33334200	Enhancers	Colon Smooth Muscle	Colon
14	chr2:33333000-33334400	Enhancers	HSMM	muscle
15	chr2:33333000-33334600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:33333000-33334600	Enhancers	HSMMtube	muscle
17	chr2:33333000-33334800	Enhancers	NHDF-Ad	bronchial
18	chr2:33333000-33336800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:33333200-33334000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:33333200-33334000	Enhancers	Aorta	Aorta
21	chr2:33333200-33334400	Enhancers	Placenta	Placenta
22	chr2:33333200-33334400	Enhancers	Left Ventricle	heart
23	chr2:33333200-33334400	Enhancers	Right Atrium	heart
24	chr2:33333200-33336600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:33333200-33336600	Enhancers	Fetal Lung	lung
26	chr2:33333400-33334200	Enhancers	Stomach Smooth Muscle	stomach
27	chr2:33333400-33346600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:33333600-33334000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:33333600-33334000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:33333600-33334000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:33333600-33334000	Enhancers	HMEC	breast
32	chr2:33333600-33334200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr2:33333600-33334200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:33333600-33334200	Enhancers	Duodenum Mucosa	Duodenum
35	chr2:33333600-33334200	Enhancers	Stomach Mucosa	stomach
36	chr2:33333600-33334400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:33333600-33334400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:33333600-33334400	Enhancers	Rectal Smooth Muscle	rectum
39	chr2:33333600-33334400	Flanking Active TSS	K562	blood
40	chr2:33333600-33334600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:33333600-33334600	Active TSS	Fetal Brain Male	brain
42	chr2:33333600-33334800	Enhancers	Fetal Stomach	stomach
43	chr2:33333600-33342200	Weak transcription	Small Intestine	intestine
44	chr2:33333800-33334200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:33333800-33334200	Flanking Active TSS	Ovary	ovary
46	chr2:33333800-33334400	Enhancers	Fetal Muscle Leg	muscle
47	chr2:33333800-33334400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr2:33333800-33336000	Weak transcription	HUVEC	blood vessel
49	chr2:33333800-33336200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:33333800-33339600	Weak transcription	Spleen	Spleen

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