Variant report

Variant	rs7254974
Chromosome Location	chr19:52212399-52212400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52205873..52210007-chr19:52211189..52216257,9	K562	blood:
2	chr19:52210196..52213453-chr19:52222345..52225170,3	K562	blood:
3	chr19:52211042..52212798-chr19:52225953..52228125,2	MCF-7	breast:
4	chr19:52211595..52213921-chr19:52286963..52288731,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182310	Chromatin interaction
ENSG00000105509	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2167416	0.87[EUR][1000 genomes]
rs2864921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35145683	0.87[EUR][1000 genomes]
rs4239495	0.88[EUR][1000 genomes]
rs4801887	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802842	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802843	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802844	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802845	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509567	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
2	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
3	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
4	nsv1064914	chr19:52103914-52231564	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	529 gene(s)	inside rSNPs	diseases
5	nsv544052	chr19:52103914-52271247	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	531 gene(s)	inside rSNPs	diseases
6	nsv1056825	chr19:52103914-52359815	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
7	nsv544053	chr19:52103914-52359815	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
8	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
9	nsv1066046	chr19:52147399-52271247	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
10	nsv544054	chr19:52147399-52271247	Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
11	nsv912296	chr19:52182363-52231032	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	518 gene(s)	inside rSNPs	diseases
12	nsv915725	chr19:52184488-52439676	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
13	nsv9742	chr19:52187538-52221742	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	517 gene(s)	inside rSNPs	diseases
14	nsv1059148	chr19:52211749-52359815	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7254974	HAS1	cis	Whole Blood	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52208000-52216600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:52208400-52212400	Strong transcription	A549	lung
3	chr19:52208400-52213000	Weak transcription	Esophagus	oesophagus
4	chr19:52208400-52213000	Weak transcription	Lung	lung
5	chr19:52208400-52216200	Weak transcription	Fetal Brain Male	brain
6	chr19:52208400-52218200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:52208400-52220200	Weak transcription	Ovary	ovary
8	chr19:52208600-52212400	Weak transcription	Colonic Mucosa	Colon
9	chr19:52208600-52212800	Weak transcription	Primary T cells from cord blood	blood
10	chr19:52208600-52212800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:52208600-52213000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:52208600-52214400	Weak transcription	Primary B cells from cord blood	blood
13	chr19:52208600-52214400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:52208600-52218800	Weak transcription	Fetal Heart	heart
15	chr19:52208800-52212400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:52208800-52213000	Weak transcription	Thymus	Thymus
17	chr19:52208800-52213000	Weak transcription	NHEK	skin
18	chr19:52208800-52213200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr19:52208800-52213600	Weak transcription	Colon Smooth Muscle	Colon
20	chr19:52208800-52214600	Weak transcription	GM12878-XiMat	blood
21	chr19:52208800-52222000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:52209000-52212400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:52209000-52214800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr19:52209600-52213800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr19:52209600-52222400	Weak transcription	Spleen	Spleen
26	chr19:52209800-52212600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:52209800-52212800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:52209800-52213000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:52210000-52213000	Weak transcription	Fetal Brain Female	brain
30	chr19:52210000-52214800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:52210200-52212400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr19:52210200-52213200	Weak transcription	Fetal Intestine Large	intestine
33	chr19:52210200-52213400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr19:52210200-52213400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:52210400-52212400	Weak transcription	Dnd41	blood
36	chr19:52210400-52212800	Weak transcription	Pancreas	Pancrea
37	chr19:52210400-52213000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:52210400-52213600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr19:52210400-52216400	Weak transcription	Brain Anterior Caudate	brain
40	chr19:52210400-52216800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr19:52210400-52218200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:52210400-52222000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:52210600-52212400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:52210600-52213400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:52210800-52213800	Weak transcription	Brain Substantia Nigra	brain
46	chr19:52210800-52215800	Weak transcription	Fetal Kidney	kidney
47	chr19:52210800-52216400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:52211000-52213000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:52211000-52214400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr19:52211000-52215000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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