Variant report

Variant	rs1196765
Chromosome Location	chr12:105608602-105608603
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	EP300	chr12:105608507-105608607	HepG2	liver:	n/a	n/a
2	NR2F2	chr12:105607848-105609787	MCF-7	breast:	n/a	n/a
3	ELF1	chr12:105608441-105609012	MCF-7	breast:	n/a	n/a
4	STAT3	chr12:105607851-105608802	MCF10A-Er-Src	breast:	n/a	chr12:105608616-105608627
5	MAZ	chr12:105608438-105608824	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr12:105608393-105608672	IMR90	lung:	n/a	n/a
7	STAT3	chr12:105607965-105609243	MCF10A-Er-Src	breast:	n/a	chr12:105608616-105608627
8	STAT3	chr12:105607843-105608858	MCF10A-Er-Src	breast:	n/a	chr12:105608616-105608627
9	TFAP2C	chr12:105608351-105608854	Hela-S3	cervix:	n/a	n/a
10	FOS	chr12:105607967-105608856	MCF10A-Er-Src	breast:	n/a	chr12:105608148-105608156
11	CHD2	chr12:105608403-105609093	Hela-S3	cervix:	n/a	n/a
12	MAX	chr12:105608004-105608832	Hela-S3	cervix:	n/a	chr12:105608047-105608057 chr12:105608043-105608052
13	ZKSCAN1	chr12:105608423-105608669	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr12:105608460-105608610	HUVEC	blood vessel:	n/a	n/a
15	FOS	chr12:105607963-105608799	MCF10A-Er-Src	breast:	n/a	chr12:105608148-105608156
16	JUN	chr12:105608012-105608640	HUVEC	blood vessel:	n/a	chr12:105608148-105608156
17	TCF12	chr12:105608361-105609016	MCF-7	breast:	n/a	n/a
18	RCOR1	chr12:105608316-105608899	Hela-S3	cervix:	n/a	n/a
19	FOS	chr12:105607865-105608919	MCF10A-Er-Src	breast:	n/a	chr12:105608148-105608156
20	CEBPB	chr12:105608165-105608846	Hela-S3	cervix:	n/a	chr12:105608280-105608293
21	CTCF	chr12:105608480-105608630	Caco-2	colon:	n/a	n/a
22	STAT3	chr12:105608249-105608787	Hela-S3	cervix:	n/a	chr12:105608616-105608627
23	TEAD4	chr12:105608415-105608800	MCF-7	breast:	n/a	n/a
24	GATA3	chr12:105608278-105608943	T-47D	breast:	n/a	n/a
25	USF2	chr12:105608469-105608646	Hela-S3	cervix:	n/a	n/a
26	SMC3	chr12:105608159-105608851	Hela-S3	cervix:	n/a	n/a
27	EP300	chr12:105608262-105608972	T-47D	breast:	n/a	n/a
28	HA-E2F1	chr12:105608465-105609179	MCF-7	breast:	n/a	n/a
29	ZNF217	chr12:105608093-105609586	MCF-7	breast:	n/a	n/a
30	EP300	chr12:105608418-105608852	MCF-7	breast:	n/a	n/a
31	GATA3	chr12:105608216-105609694	T-47D	breast:	n/a	n/a
32	POLR2A	chr12:105607905-105608931	MCF10A-Er-Src	breast:	n/a	n/a
33	MYC	chr12:105607870-105608861	MCF10A-Er-Src	breast:	n/a	chr12:105608047-105608057 chr12:105608043-105608052
34	HDAC2	chr12:105608429-105608907	MCF-7	breast:	n/a	n/a
35	GATA3	chr12:105608297-105609655	MCF-7	breast:	n/a	n/a
36	CEBPB	chr12:105607829-105608873	MCF-7	breast:	n/a	chr12:105608280-105608293
37	GATA3	chr12:105608364-105609553	MCF-7	breast:	n/a	n/a
38	TCF7L2	chr12:105608300-105608870	MCF-7	breast:	n/a	n/a
39	RAD21	chr12:105608332-105608840	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr12:105608351-105608694	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr12:105608087-105608745	HUVEC	blood vessel:	n/a	n/a
42	SIN3AK20	chr12:105607737-105609726	MCF-7	breast:	n/a	n/a
43	GTF2F1	chr12:105608368-105608857	Hela-S3	cervix:	n/a	n/a
44	EP300	chr12:105608328-105608872	Hela-S3	cervix:	n/a	n/a
45	GATA2	chr12:105608220-105608872	HUVEC	blood vessel:	n/a	n/a
46	CEBPB	chr12:105608350-105608671	HepG2	liver:	n/a	n/a
47	GATA3	chr12:105607875-105609773	MCF-7	breast:	n/a	chr12:105608184-105608193
48	EP300	chr12:105608319-105608923	T-47D	breast:	n/a	n/a
49	TCF7L2	chr12:105608344-105608990	Hela-S3	cervix:	n/a	n/a
50	NR2F2	chr12:105608179-105609576	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:105607304..105609527-chr12:105723338..105725728,2	MCF-7	breast:
2	chr12:105501422..105503562-chr12:105608423..105610224,2	MCF-7	breast:
3	chr12:105606486..105608815-chr12:105609324..105611383,2	K562	blood:
4	chr12:105567931..105571884-chr12:105607203..105610090,3	MCF-7	breast:
5	chr12:105606787..105609967-chr12:105617120..105620044,3	MCF-7	breast:
6	chr12:105501251..105503302-chr12:105608033..105610589,2	MCF-7	breast:
7	chr12:105608225..105613366-chr12:105619333..105624104,5	MCF-7	breast:
8	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:

Variant related genes	Relation type
APPL2	TF binding region
ENSG00000235162	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10746010	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778367	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778368	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778369	0.84[EUR][1000 genomes]
rs1107755	0.85[EUR][1000 genomes]
rs1107757	0.85[EUR][1000 genomes]
rs11112424	0.85[EUR][1000 genomes]
rs11112434	0.85[EUR][1000 genomes]
rs11112467	1.00[ASN][1000 genomes]
rs1196742	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196745	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196748	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196749	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196753	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196754	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196756	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[ASN][1000 genomes]
rs1196764	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196770	0.94[EUR][1000 genomes]
rs1196772	0.94[EUR][1000 genomes]
rs1196777	0.93[EUR][1000 genomes]
rs1196780	0.86[EUR][1000 genomes]
rs1196782	0.85[EUR][1000 genomes]
rs1196786	0.84[EUR][1000 genomes]
rs1196787	0.84[EUR][1000 genomes]
rs1196789	0.84[EUR][1000 genomes]
rs1196793	0.85[EUR][1000 genomes]
rs1196795	0.83[EUR][1000 genomes]
rs1196797	0.84[EUR][1000 genomes]
rs1196798	0.97[EUR][1000 genomes]
rs1196800	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196801	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196805	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196806	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196807	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196808	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196811	0.97[EUR][1000 genomes]
rs1196813	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196817	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196819	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196820	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196823	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196825	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196831	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196833	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196834	0.81[EUR][1000 genomes]
rs1196839	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196841	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196842	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196844	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196847	0.83[EUR][1000 genomes]
rs1196848	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196851	0.96[EUR][1000 genomes]
rs1196853	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196861	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196862	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196864	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196869	0.97[EUR][1000 genomes]
rs1196871	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196872	0.96[EUR][1000 genomes]
rs1196873	0.97[EUR][1000 genomes]
rs1196874	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196881	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196884	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196885	0.83[EUR][1000 genomes]
rs1206559	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209308	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209637	0.84[EUR][1000 genomes]
rs1211276	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211277	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211626	0.84[EUR][1000 genomes]
rs12369709	0.83[EUR][1000 genomes]
rs12814458	0.85[EUR][1000 genomes]
rs12816560	0.86[EUR][1000 genomes]
rs1345096	0.88[EUR][1000 genomes]
rs1444610	0.84[EUR][1000 genomes]
rs1621553	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[ASN][1000 genomes]
rs1663565	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732370	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166142	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246243	0.89[EUR][1000 genomes]
rs2257156	0.96[EUR][1000 genomes]
rs2374449	0.86[EUR][1000 genomes]
rs2440692	0.87[EUR][1000 genomes]
rs2440714	0.93[EUR][1000 genomes]
rs2440715	1.00[ASN][1000 genomes]
rs2440718	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464173	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464175	0.97[EUR][1000 genomes]
rs2464181	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464182	0.95[EUR][1000 genomes]
rs35679386	0.86[EUR][1000 genomes]
rs4356312	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356313	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372534	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390426	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545651	1.00[ASN][1000 genomes]
rs4964122	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964331	0.86[EUR][1000 genomes]
rs6539183	0.82[EUR][1000 genomes]
rs6539186	0.83[EUR][1000 genomes]
rs6539187	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539188	0.86[EUR][1000 genomes]
rs7132040	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.88[EUR][1000 genomes]
rs7132855	0.88[EUR][1000 genomes]
rs71441895	0.94[EUR][1000 genomes]
rs7299225	1.00[ASN][1000 genomes]
rs7299701	0.85[EUR][1000 genomes]
rs7302854	0.83[EUR][1000 genomes]
rs7303961	0.90[EUR][1000 genomes]
rs73181823	0.86[EUR][1000 genomes]
rs7959385	1.00[ASN][1000 genomes]
rs7963877	0.82[EUR][1000 genomes]
rs873119	0.85[EUR][1000 genomes]
rs935240	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935241	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935242	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935244	0.94[EUR][1000 genomes]
rs935246	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935248	0.97[EUR][1000 genomes]
rs935249	0.96[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	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1196765	LOC414300	cis	brain	BrainEAC
rs1196765	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105571400-105617800	Weak transcription	K562	blood
4	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr12:105579000-105612400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr12:105580200-105613200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:105587400-105609000	Weak transcription	Fetal Brain Male	brain
11	chr12:105589200-105612200	Weak transcription	Psoas Muscle	Psoas
12	chr12:105589400-105612400	Weak transcription	Fetal Heart	heart
13	chr12:105590200-105620000	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:105590400-105618800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr12:105591000-105619400	Strong transcription	Primary T cells from cord blood	blood
16	chr12:105594400-105614400	Weak transcription	Small Intestine	intestine
17	chr12:105595000-105612800	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:105595000-105618800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:105595600-105612800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:105595800-105612000	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:105595800-105612200	Weak transcription	Right Atrium	heart
22	chr12:105595800-105616600	Strong transcription	Primary hematopoietic stem cells	blood
23	chr12:105596000-105617000	Strong transcription	Fetal Lung	lung
24	chr12:105596400-105621800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:105599400-105612400	Strong transcription	Brain Anterior Caudate	brain
26	chr12:105599800-105610800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:105600800-105610000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:105600800-105626800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:105601000-105612400	Strong transcription	Fetal Stomach	stomach
30	chr12:105601000-105615800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:105601000-105619200	Weak transcription	GM12878-XiMat	blood
32	chr12:105601200-105610200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:105601200-105610400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:105601400-105610400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:105601400-105615800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:105602000-105610400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:105602200-105612000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:105604000-105611800	Strong transcription	Left Ventricle	heart
39	chr12:105604200-105611600	Strong transcription	Ovary	ovary
40	chr12:105604200-105616200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:105604400-105611600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr12:105604400-105612400	Strong transcription	Lung	lung
43	chr12:105604400-105613000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:105604400-105618400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:105604600-105611200	Strong transcription	Brain Angular Gyrus	brain
46	chr12:105604800-105609000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:105604800-105609200	Genic enhancers	HSMM	muscle
48	chr12:105604800-105610200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:105605200-105608800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:105605400-105610200	Weak transcription	Esophagus	oesophagus

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