Variant report

Variant	rs73107993
Chromosome Location	chr12:48195873-48195874
allele	C/T
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	chr12:48195620-48195949	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr12:48195840-48195990	HRE	kidney:	n/a	chr12:48195870-48195888 chr12:48195872-48195885
3	POLR2A	chr12:48195569-48196594	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr12:48195295-48197895	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr12:48195081-48195905	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr12:48195800-48195950	WI-38	lung:	n/a	chr12:48195870-48195888 chr12:48195872-48195885
7	CTCF	chr12:48195820-48195970	NHDF-neo	bronchial:	n/a	chr12:48195870-48195888 chr12:48195872-48195885
8	CTCF	chr12:48195800-48195950	GM12871	blood:	n/a	chr12:48195870-48195888 chr12:48195872-48195885
9	FOXP2	chr12:48195637-48195945	PFSK-1	brain:	n/a	n/a
10	CTCF	chr12:48195780-48195930	GM12864	blood:	n/a	chr12:48195870-48195888 chr12:48195872-48195885
11	STAT3	chr12:48195796-48195938	MCF10A-Er-Src	breast:	n/a	n/a
12	CTCF	chr12:48195760-48195910	HUVEC	blood vessel:	n/a	chr12:48195870-48195888 chr12:48195872-48195885
13	POLR2A	chr12:48195682-48196059	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48194186..48196955-chr12:48205034..48206864,2	K562	blood:
2	chr12:48188175..48191554-chr12:48193435..48196727,4	K562	blood:
3	chr12:48166395..48169503-chr12:48195683..48198388,3	MCF-7	breast:
4	chr12:48195484..48196001-chr12:48231023..48231696,2	MCF-7	breast:
5	chr12:48178200..48181079-chr12:48195107..48197877,2	K562	blood:
6	chr12:48194186..48197622-chr12:48205034..48208393,5	K562	blood:
7	chr12:48194244..48196196-chr12:48197765..48200382,2	MCF-7	breast:
8	chr12:48189801..48192415-chr12:48195227..48196888,2	K562	blood:

Variant related genes	Relation type
HDAC7	TF binding region
ENSG00000061273	Chromatin interaction
ENSG00000268069	Chromatin interaction
ENSG00000211584	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11168244	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11168245	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11168250	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168251	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168252	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2544026	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55726902	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56389811	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73107980	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs875023	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers 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	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription 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 miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	esv3693398	chr12:48186738-48215749	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73107993	HDAC7	cis	brain	BrainEAC

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48177800-48196000	Strong transcription	NHEK	skin
2	chr12:48178600-48199200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:48179800-48201000	Weak transcription	Dnd41	blood
4	chr12:48181200-48199800	Strong transcription	Fetal Intestine Small	intestine
5	chr12:48182000-48206400	Weak transcription	HepG2	liver
6	chr12:48182400-48202000	Weak transcription	Fetal Brain Male	brain
7	chr12:48183000-48204000	Weak transcription	Fetal Kidney	kidney
8	chr12:48188600-48196600	Weak transcription	K562	blood
9	chr12:48189000-48201000	Weak transcription	NH-A	brain
10	chr12:48190800-48201400	Genic enhancers	Fetal Thymus	thymus
11	chr12:48191000-48197200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:48191000-48201200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:48191400-48197200	Enhancers	Brain Angular Gyrus	brain
14	chr12:48191400-48200000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:48191400-48200200	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr12:48191400-48200600	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr12:48191400-48201400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:48191400-48202800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:48191600-48196800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:48191600-48201600	Genic enhancers	Thymus	Thymus
21	chr12:48191800-48196200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:48192000-48196800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:48192000-48198000	Enhancers	Brain Anterior Caudate	brain
24	chr12:48192200-48200200	Genic enhancers	Lung	lung
25	chr12:48192400-48196200	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr12:48192400-48196800	Enhancers	Psoas Muscle	Psoas
27	chr12:48192400-48201000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr12:48192400-48201600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr12:48192400-48203200	Enhancers	Right Atrium	heart
30	chr12:48192600-48196200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:48192600-48196400	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr12:48192600-48197000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:48192600-48198000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:48192600-48198800	Weak transcription	Fetal Brain Female	brain
35	chr12:48192600-48201400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr12:48192800-48197600	Enhancers	Left Ventricle	heart
37	chr12:48192800-48200200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:48192800-48200200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:48193000-48197200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:48193000-48200400	Genic enhancers	Fetal Muscle Leg	muscle
41	chr12:48193200-48197200	Enhancers	Colon Smooth Muscle	Colon
42	chr12:48193200-48198000	Enhancers	Duodenum Mucosa	Duodenum
43	chr12:48193200-48200000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:48193200-48200200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr12:48193200-48200200	Enhancers	Pancreas	Pancrea
46	chr12:48193400-48197600	Enhancers	Placenta	Placenta
47	chr12:48193400-48197800	Enhancers	NHDF-Ad	bronchial
48	chr12:48193400-48198200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:48193400-48200200	Enhancers	Brain Substantia Nigra	brain
50	chr12:48193400-48203000	Enhancers	Fetal Heart	heart

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