Variant report

Variant	rs12608744
Chromosome Location	chr19:18375563-18375564
allele	A/G
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	chr19:18374079-18378644	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18375043..18380039-chr19:18389478..18393263,5	MCF-7	breast:
2	chr19:18330088..18331669-chr19:18374147..18376763,2	K562	blood:
3	chr19:18374800..18379713-chr19:18383305..18387189,5	MCF-7	breast:
4	chr19:18374562..18377153-chr19:18385141..18387044,2	MCF-7	breast:
5	chr19:18356349..18358578-chr19:18375314..18377144,2	K562	blood:

Variant related genes	Relation type
KIAA1683	TF binding region
ENSG00000130518	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000267959	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1035363	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11086099	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12459276	0.95[ASN][1000 genomes]
rs12460547	0.92[ASN][1000 genomes]
rs12461561	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12608843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12608869	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1477269	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1477271	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2287656	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287657	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2384989	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35768432	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810432	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810433	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810434	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808776	0.93[ASN][1000 genomes]
rs58555271	0.95[ASN][1000 genomes]
rs60452015	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60609985	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62120402	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72479531	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73523118	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73523119	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8105176	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105503	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109771	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113654	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9710173	0.84[ASN][1000 genomes]
rs9710599	0.86[ASN][1000 genomes]
rs999814	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs999815	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
3	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
7	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
8	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
9	nsv911260	chr19:18288069-18386798	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv470131	chr19:18326222-18389135	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
11	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
12	nsv911266	chr19:18351674-18375659	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv911267	chr19:18351674-18386798	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv911268	chr19:18351674-18395537	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
15	nsv911269	chr19:18351674-18418044	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
16	nsv911270	chr19:18351674-18422364	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
17	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12608744	KIAA1683	cis	Thyroid	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18348600-18385200	Weak transcription	Right Atrium	heart
2	chr19:18365600-18375600	Weak transcription	Brain Substantia Nigra	brain
3	chr19:18366000-18377200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:18366400-18375800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:18366400-18376800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:18366400-18389400	Weak transcription	Fetal Brain Male	brain
7	chr19:18366600-18377400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr19:18366600-18385400	Weak transcription	Primary B cells from cord blood	blood
9	chr19:18366600-18385800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr19:18366600-18390000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:18367200-18375800	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:18367600-18380400	Strong transcription	Fetal Muscle Leg	muscle
13	chr19:18367600-18381600	Strong transcription	Fetal Intestine Small	intestine
14	chr19:18367800-18380800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr19:18369600-18380400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr19:18371000-18385400	Weak transcription	HSMMtube	muscle
17	chr19:18371400-18376600	Weak transcription	NHDF-Ad	bronchial
18	chr19:18371400-18376800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:18372200-18380400	Strong transcription	Ovary	ovary
20	chr19:18372400-18379800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:18373000-18376000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr19:18373000-18379200	Strong transcription	Esophagus	oesophagus
23	chr19:18373200-18376200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr19:18373200-18380400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr19:18373400-18377000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:18373400-18379800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:18373400-18380400	Strong transcription	Brain Anterior Caudate	brain
28	chr19:18373400-18380400	Strong transcription	Fetal Brain Female	brain
29	chr19:18373400-18380400	Strong transcription	Fetal Intestine Large	intestine
30	chr19:18373400-18380400	Strong transcription	Lung	lung
31	chr19:18373400-18380800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:18373600-18377200	Genic enhancers	Spleen	Spleen
33	chr19:18373600-18378600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:18373600-18378600	Strong transcription	Brain Germinal Matrix	brain
35	chr19:18373600-18380600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:18373800-18376000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:18373800-18376200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:18373800-18377000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr19:18373800-18378600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:18373800-18379200	Strong transcription	Primary T cells from cord blood	blood
41	chr19:18373800-18380400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:18373800-18380400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr19:18374000-18375600	Weak transcription	Fetal Lung	lung
44	chr19:18374000-18377400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:18374000-18377400	Weak transcription	Left Ventricle	heart
46	chr19:18374000-18379400	Strong transcription	Placenta	Placenta
47	chr19:18374000-18379800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr19:18374200-18379400	Strong transcription	Gastric	stomach
49	chr19:18374400-18375800	Enhancers	K562	blood
50	chr19:18374400-18378600	Strong transcription	Stomach Mucosa	stomach

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