Variant report

Variant	rs1493796
Chromosome Location	chr12:74931349-74931350
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	chr12:74931300-74932160	ProgFib	skin:	n/a	n/a
2	CTCF	chr12:74931220-74931370	NHEK	skin:	n/a	n/a
3	POLR2A	chr12:74931200-74936073	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:74931310-74933110	HL-60	blood:	n/a	n/a
5	POLR2A	chr12:74931151-74933337	GM18505	blood:	n/a	n/a
6	TBP	chr12:74931073-74931985	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:74931170-74932166	SK-N-MC	brain:	n/a	n/a
8	CTCF	chr12:74930926-74931382	MCF-7	breast:	n/a	chr12:74931174-74931187 chr12:74931167-74931188 chr12:74931172-74931190 chr12:74931177-74931185 chr12:74931173-74931189
9	CHD1	chr12:74930901-74933411	IMR90	lung:	n/a	n/a
10	RAD21	chr12:74930749-74932031	SK-N-SH	brain:	n/a	chr12:74931180-74931187 chr12:74931170-74931189
11	ETS1	chr12:74931007-74932114	A549	lung:	n/a	chr12:74931564-74931575 chr12:74931773-74931784
12	TBP	chr12:74931189-74932928	K562	blood:	n/a	n/a
13	FOXM1	chr12:74930964-74932043	GM12878	blood:	n/a	n/a
14	HA-E2F1	chr12:74931278-74933877	MCF-7	breast:	n/a	chr12:74931774-74931784 chr12:74931773-74931782 chr12:74931642-74931649 chr12:74931547-74931556
15	SIN3AK20	chr12:74930955-74931707	A549	lung:	n/a	n/a
16	SIN3A	chr12:74931173-74932770	H1-hESC	embryonic stem cell:	n/a	chr12:74931816-74931829
17	PML	chr12:74931166-74931789	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:74931300-74932673	HL-60	blood:	n/a	n/a
19	POLR2A	chr12:74931030-74932264	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr12:74931348-74932116	K562	blood:	n/a	n/a
21	MYC	chr12:74931344-74931757	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr12:74931029-74931379	HUVEC	blood vessel:	n/a	chr12:74931174-74931187 chr12:74931167-74931188 chr12:74931172-74931190 chr12:74931177-74931185 chr12:74931173-74931189
23	RAD21	chr12:74930761-74931905	HCT-116	colon:	n/a	chr12:74931180-74931187 chr12:74931170-74931189
24	TAF1	chr12:74931300-74932239	ECC-1	luminal epithelium:	n/a	n/a
25	CHD2	chr12:74931121-74931881	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:74931347-74932205	H1-hESC	embryonic stem cell:	n/a	n/a
27	REST	chr12:74930995-74932711	H1-neurons	neurons:	n/a	chr12:74931502-74931522 chr12:74931502-74931522 chr12:74931816-74931836
28	POLR2A	chr12:74931260-74932776	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:74931069-74932593	GM19099	blood:	n/a	n/a
30	MXI1	chr12:74930680-74934315	SK-N-SH	brain:	n/a	chr12:74932789-74932798
31	POLR2A	chr12:74931124-74932000	U87	brain:	n/a	n/a
32	MAX	chr12:74931344-74932273	SK-N-SH	brain:	n/a	n/a
33	JUND	chr12:74931004-74932543	K562	blood:	n/a	chr12:74931646-74931654 chr12:74931647-74931658
34	POLR2A	chr12:74931298-74931916	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr12:74931241-74932044	GM12892	blood:	n/a	n/a
36	GABPA	chr12:74931295-74932064	SK-N-SH	brain:	n/a	chr12:74931546-74931555 chr12:74931543-74931557 chr12:74931546-74931560 chr12:74931546-74931557
37	PBX3	chr12:74931003-74931950	SK-N-SH	brain:	n/a	chr12:74931795-74931815
38	STAT1	chr12:74931177-74932082	GM12878	blood:	n/a	n/a
39	MTA3	chr12:74931106-74932309	GM12878	blood:	n/a	n/a
40	EBF1	chr12:74931084-74931843	GM12878	blood:	n/a	chr12:74931610-74931621
41	CTCF	chr12:74931260-74931410	WI-38	lung:	n/a	n/a
42	POLR2A	chr12:74931172-74932362	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr12:74931120-74932122	PANC-1	pancreas:	n/a	n/a
44	NRF1	chr12:74931336-74931757	H1-hESC	embryonic stem cell:	n/a	chr12:74931546-74931555 chr12:74931545-74931556 chr12:74931543-74931557 chr12:74931527-74931538 chr12:74931546-74931560 chr12:74931546-74931557
45	MYC	chr12:74931057-74933117	K562	blood:	n/a	chr12:74932790-74932800 chr12:74932789-74932800 chr12:74932790-74932799 chr12:74932788-74932801 chr12:74932790-74932800 chr12:74932788-74932801 chr12:74932786-74932801 chr12:74932789-74932800 chr12:74932791-74932800 chr12:74932792-74932799 chr12:74932789-74932800 chr12:74932789-74932798 chr12:74932788-74932801
46	BHLHE40	chr12:74931042-74932197	GM12878	blood:	n/a	n/a
47	TCF7L2	chr12:74931076-74933168	Hela-S3	cervix:	n/a	chr12:74932622-74932638
48	ZNF143	chr12:74931004-74931983	K562	blood:	n/a	n/a
49	KAP1	chr12:74931080-74931604	K562	blood:	n/a	n/a
50	NFIC	chr12:74931265-74932402	SK-N-SH	brain:	n/a	chr12:74932066-74932082 chr12:74932066-74932083

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:74687125..74689371-chr12:74929648..74931476,2	K562	blood:

Variant related genes	Relation type
ATXN7L3B	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10506693	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12809241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12825946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1493801	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1493810	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17113674	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17113675	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17113679	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17113748	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17113750	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17180010	1.00[JPT][hapmap]
rs1824539	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2061579	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2126136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2605375	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2605381	0.98[ASN][1000 genomes]
rs2613902	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2641470	0.80[ASN][1000 genomes]
rs2641471	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34706013	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35454023	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35957931	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36030036	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36153793	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4547177	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882643	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58783285	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs590352	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs60905363	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67506065	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7132047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs725181	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7295970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7300059	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7304361	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7957387	1.00[JPT][hapmap]
rs7962722	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7964349	1.00[JPT][hapmap]
rs9668146	0.88[EUR][1000 genomes];0.92[ASN][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	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv899292	chr12:74835107-74934162	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv899293	chr12:74835107-74995760	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv559414	chr12:74850206-74931349	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	nsv899295	chr12:74854750-74984992	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv559417	chr12:74857957-74931349	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
7	nsv470303	chr12:74880668-74945356	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	n/a
8	nsv899296	chr12:74880668-74974630	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1493796	LRRC10	cis	cerebellum	SCAN
rs1493796	GLIPR1L1	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74930200-74932400	Active TSS	A549	lung
2	chr12:74930600-74931800	Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr12:74930600-74932400	Active TSS	Placenta	Placenta
4	chr12:74930600-74932400	Active TSS	Psoas Muscle	Psoas
5	chr12:74930600-74932400	Active TSS	HSMM	muscle
6	chr12:74930600-74932800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:74930800-74931400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr12:74930800-74931400	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr12:74930800-74931400	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr12:74930800-74931400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr12:74930800-74931800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr12:74930800-74931800	Active TSS	Muscle Satellite Cultured Cells	--
13	chr12:74930800-74931800	Active TSS	Brain Germinal Matrix	brain
14	chr12:74930800-74931800	Active TSS	HepG2	liver
15	chr12:74930800-74932000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr12:74930800-74932000	Active TSS	Adipose Nuclei	Adipose
17	chr12:74930800-74932000	Active TSS	Stomach Smooth Muscle	stomach
18	chr12:74930800-74932200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:74930800-74932200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr12:74930800-74932200	Active TSS	Fetal Muscle Leg	muscle
21	chr12:74930800-74932200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr12:74930800-74932200	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr12:74930800-74932200	Active TSS	NH-A	brain
24	chr12:74930800-74932200	Active TSS	Osteobl	bone
25	chr12:74930800-74932400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:74930800-74932400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:74930800-74932400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:74930800-74932400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:74930800-74932400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:74930800-74932400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:74930800-74932400	Active TSS	Colon Smooth Muscle	Colon
32	chr12:74930800-74932400	Active TSS	Duodenum Mucosa	Duodenum
33	chr12:74930800-74932400	Active TSS	Fetal Brain Female	brain
34	chr12:74930800-74932400	Active TSS	Fetal Thymus	thymus
35	chr12:74930800-74932400	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr12:74930800-74932400	Active TSS	Thymus	Thymus
37	chr12:74930800-74932400	Active TSS	Hela-S3	cervix
38	chr12:74930800-74932400	Active TSS	HMEC	breast
39	chr12:74930800-74932400	Active TSS	HSMMtube	muscle
40	chr12:74930800-74932400	Active TSS	NHDF-Ad	bronchial
41	chr12:74930800-74932400	Active TSS	NHEK	skin
42	chr12:74930800-74932400	Active TSS	NHLF	lung
43	chr12:74930800-74932600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:74930800-74932600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:74930800-74932600	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr12:74930800-74932600	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr12:74930800-74932600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:74930800-74932600	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr12:74930800-74932600	Active TSS	Placenta Amnion	Placenta Amnion
50	chr12:74930800-74932600	Active TSS	GM12878-XiMat	blood

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