Variant report

Variant	rs10128967
Chromosome Location	chr12:48452709-48452710
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	KAP1	chr12:48452253-48453303	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48435313..48437988-chr12:48451982..48454529,2	K562	blood:

Variant related genes	Relation type
ENSG00000240399	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10128968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506276	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10875718	1.00[CHB][hapmap]
rs10875719	1.00[CHB][hapmap]
rs11574026	1.00[CHB][hapmap]
rs11830378	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12297820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12301562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316682	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17224674	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs17224828	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17225198	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17607800	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs17823193	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17823415	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs17823565	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs41291963	1.00[ASN][1000 genomes]
rs41291967	1.00[ASN][1000 genomes]
rs55820056	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56345199	0.88[EUR][1000 genomes]
rs57956448	1.00[ASN][1000 genomes]
rs58317398	1.00[ASN][1000 genomes]
rs60209369	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60679254	1.00[ASN][1000 genomes]
rs7297558	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7301153	0.81[CEU][hapmap]
rs7301509	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7307874	0.81[CEU][hapmap]
rs7310935	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs73301106	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73301111	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73304917	1.00[ASN][1000 genomes]
rs74089110	1.00[ASN][1000 genomes]
rs74089159	1.00[ASN][1000 genomes]
rs74089163	1.00[ASN][1000 genomes]
rs9630296	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10128967	DDN	cis	parietal	SCAN
rs10128967	NCKAP5L	cis	parietal	SCAN
rs10128967	LOC255411	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48431800-48456600	Weak transcription	NHLF	lung
2	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
5	chr12:48435400-48457200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:48439200-48453000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:48439200-48456800	Weak transcription	HMEC	breast
9	chr12:48439200-48468000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:48439600-48455400	Weak transcription	Colonic Mucosa	Colon
11	chr12:48440000-48454000	Weak transcription	HUVEC	blood vessel
12	chr12:48440000-48457200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:48440200-48453800	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:48440400-48453400	Weak transcription	Esophagus	oesophagus
15	chr12:48441200-48457000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:48441400-48453400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:48441400-48453400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:48441400-48454400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
20	chr12:48441600-48452800	Weak transcription	NHEK	skin
21	chr12:48441600-48468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:48443000-48453200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:48443400-48453400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:48443400-48453600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:48444000-48452800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:48444200-48474600	Weak transcription	Gastric	stomach
28	chr12:48444800-48453000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:48444800-48468000	Weak transcription	Spleen	Spleen
30	chr12:48446000-48453800	Weak transcription	Brain Angular Gyrus	brain
31	chr12:48449400-48452800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:48449400-48453400	Weak transcription	Aorta	Aorta
33	chr12:48449400-48453400	Weak transcription	Ovary	ovary
34	chr12:48449400-48453600	Weak transcription	Fetal Stomach	stomach
35	chr12:48449400-48453600	Weak transcription	Lung	lung
36	chr12:48449400-48453600	Weak transcription	Pancreas	Pancrea
37	chr12:48449400-48464400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:48452000-48452800	Strong transcription	HSMM	muscle
39	chr12:48452000-48453000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:48452000-48453600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:48452000-48453800	Weak transcription	Fetal Intestine Small	intestine
42	chr12:48452000-48453800	ZNF genes & repeats	A549	lung
43	chr12:48452000-48460200	Strong transcription	Hela-S3	cervix
44	chr12:48452000-48468600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:48452000-48468800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:48452000-48468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:48452000-48469400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:48452200-48452800	ZNF genes & repeats	Brain Hippocampus Middle	brain
49	chr12:48452200-48452800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
50	chr12:48452200-48452800	ZNF genes & repeats	HepG2	liver

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