Variant report

Variant	rs875023
Chromosome Location	chr12:48194435-48194436
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	CEBPB	chr12:48194378-48194627	HepG2	liver:	n/a	chr12:48194475-48194486 chr12:48194476-48194487
2	POLR2A	chr12:48194078-48195028	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:48193017-48194842	K562	blood:	n/a	n/a
4	POLR2A	chr12:48194303-48194635	HUVEC	blood vessel:	n/a	n/a
5	CEBPB	chr12:48194401-48194601	K562	blood:	n/a	chr12:48194475-48194486 chr12:48194476-48194487

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	chr12:48193420..48195604-chr12:48198612..48200670,2	K562	blood:
4	chr12:48194186..48197622-chr12:48205034..48208393,5	K562	blood:
5	chr12:48194244..48196196-chr12:48197765..48200382,2	MCF-7	breast:
6	chr12:48177447..48181370-chr12:48191436..48194487,4	K562	blood:

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

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11168244	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11168245	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11168250	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11168251	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11168252	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs55726902	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56389811	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7135791	1.00[LWK][hapmap]
rs73107980	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73107993	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs875023	HDAC7	cis	cerebellum	SCAN
rs875023	ENDOU	cis	parietal	SCAN
rs875023	RAPGEF3	cis	parietal	SCAN
rs875023	MLL2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48168200-48195200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:48173800-48195400	Strong transcription	Fetal Stomach	stomach
3	chr12:48174600-48195600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48174800-48194600	Strong transcription	Fetal Intestine Large	intestine
5	chr12:48175600-48195000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:48175600-48195800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:48177800-48196000	Strong transcription	NHEK	skin
8	chr12:48178600-48199200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:48179600-48194800	Weak transcription	Small Intestine	intestine
10	chr12:48179600-48195400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:48179800-48201000	Weak transcription	Dnd41	blood
12	chr12:48181200-48199800	Strong transcription	Fetal Intestine Small	intestine
13	chr12:48182000-48195800	Weak transcription	GM12878-XiMat	blood
14	chr12:48182000-48206400	Weak transcription	HepG2	liver
15	chr12:48182400-48202000	Weak transcription	Fetal Brain Male	brain
16	chr12:48183000-48204000	Weak transcription	Fetal Kidney	kidney
17	chr12:48186000-48195600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:48186400-48194800	Weak transcription	HMEC	breast
19	chr12:48186400-48195400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:48188400-48195400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:48188600-48196600	Weak transcription	K562	blood
22	chr12:48188800-48195200	Weak transcription	Fetal Lung	lung
23	chr12:48189000-48195200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:48189000-48201000	Weak transcription	NH-A	brain
25	chr12:48189800-48194800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:48190800-48201400	Genic enhancers	Fetal Thymus	thymus
27	chr12:48191000-48197200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:48191000-48201200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:48191200-48195200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:48191200-48195400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:48191400-48197200	Enhancers	Brain Angular Gyrus	brain
32	chr12:48191400-48200000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:48191400-48200200	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr12:48191400-48200600	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr12:48191400-48201400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:48191400-48202800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:48191600-48194800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:48191600-48195000	Weak transcription	Liver	Liver
39	chr12:48191600-48196800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:48191600-48201600	Genic enhancers	Thymus	Thymus
41	chr12:48191800-48195400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:48191800-48196200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:48192000-48195200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr12:48192000-48195400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:48192000-48195600	Weak transcription	A549	lung
46	chr12:48192000-48196800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:48192000-48198000	Enhancers	Brain Anterior Caudate	brain
48	chr12:48192200-48195400	Genic enhancers	Spleen	Spleen
49	chr12:48192200-48200200	Genic enhancers	Lung	lung
50	chr12:48192400-48194800	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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