Variant report

Variant	rs35828893
Chromosome Location	chr19:37832608-37832609
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:37832596-37832655	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37825994..37829607-chr19:37831391..37834553,3	MCF-7	breast:

Variant related genes	Relation type
HKR1	TF binding region
ENSG00000267682	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12986074	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12986146	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17243193	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34490389	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3745764	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][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	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35828893	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37826200-37853200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37826400-37832800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:37826400-37834600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:37826400-37835200	Weak transcription	Aorta	Aorta
5	chr19:37826400-37837800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:37826400-37838200	Weak transcription	HUVEC	blood vessel
7	chr19:37826600-37834200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:37826600-37834400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:37826600-37834800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr19:37826600-37835600	Weak transcription	Osteobl	bone
11	chr19:37826600-37838000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:37826600-37848800	Weak transcription	Small Intestine	intestine
13	chr19:37826600-37856200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:37826600-37861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:37826800-37833800	Weak transcription	Adipose Nuclei	Adipose
16	chr19:37826800-37834400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:37826800-37834600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:37826800-37834800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:37826800-37835000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:37826800-37836200	Weak transcription	Gastric	stomach
21	chr19:37826800-37838000	Weak transcription	Psoas Muscle	Psoas
22	chr19:37826800-37846600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:37826800-37847000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:37826800-37852600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:37826800-37853400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:37827000-37834400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:37827000-37834400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:37827000-37834600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:37827000-37834600	Weak transcription	Fetal Brain Female	brain
30	chr19:37827000-37834800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:37827000-37834800	Weak transcription	Spleen	Spleen
32	chr19:37827000-37835200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:37827000-37835200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr19:37827000-37835400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:37827000-37837000	Weak transcription	Colon Smooth Muscle	Colon
36	chr19:37827000-37837000	Weak transcription	NHLF	lung
37	chr19:37827000-37838000	Weak transcription	Pancreas	Pancrea
38	chr19:37827000-37838400	Weak transcription	Hela-S3	cervix
39	chr19:37827000-37845800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr19:37827000-37853400	Weak transcription	Stomach Mucosa	stomach
41	chr19:37827200-37833800	Weak transcription	Right Ventricle	heart
42	chr19:37827200-37833800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr19:37827200-37834400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:37827200-37834800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr19:37827200-37837200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr19:37827200-37838600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr19:37828000-37833000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:37828000-37833000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr19:37828000-37833800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:37828000-37855800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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