Variant report

Variant	rs1196777
Chromosome Location	chr12:105625440-105625441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:105625300-105625450	AG10803	skin:	n/a	n/a
2	RAD21	chr12:105625301-105625479	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr12:105625300-105625450	Caco-2	colon:	n/a	n/a
4	CTCF	chr12:105625340-105625490	HepG2	liver:	n/a	n/a
5	RAD21	chr12:105625362-105625517	HepG2	liver:	n/a	n/a
6	CTCF	chr12:105625321-105625444	MCF-7	breast:	n/a	n/a
7	CTCF	chr12:105625320-105625470	RPTEC	kidney:	n/a	n/a
8	RCOR1	chr12:105625396-105625578	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:
2	chr12:105624829..105626862-chr12:105636321..105638776,2	MCF-7	breast:

No data

Variant related genes	Relation type
APPL2	TF binding region
C12orf75	TF binding region
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10746010	0.82[EUR][1000 genomes]
rs10778367	1.00[CHB][hapmap]
rs10861347	1.00[CHB][hapmap]
rs10861371	1.00[CHB][hapmap]
rs10861400	1.00[CHB][hapmap]
rs10861407	1.00[CHB][hapmap]
rs10861409	1.00[CHB][hapmap]
rs1107755	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107757	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112424	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112428	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11112434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112475	1.00[CHB][hapmap]
rs1196742	0.92[EUR][1000 genomes]
rs1196745	0.92[EUR][1000 genomes]
rs1196748	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs1196749	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs1196753	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs1196754	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs1196756	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs1196760	1.00[CHB][hapmap]
rs1196764	0.92[EUR][1000 genomes]
rs1196765	0.93[EUR][1000 genomes]
rs1196770	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196772	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196780	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1196782	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196786	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196787	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1196789	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1196790	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1196791	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196793	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196795	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1196797	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196798	0.90[EUR][1000 genomes]
rs1196800	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196801	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196805	0.91[EUR][1000 genomes]
rs1196806	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196807	0.91[EUR][1000 genomes]
rs1196808	0.90[EUR][1000 genomes]
rs1196811	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs1196813	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196817	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196818	1.00[CHB][hapmap]
rs1196819	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196820	0.91[EUR][1000 genomes]
rs1196823	0.90[EUR][1000 genomes]
rs1196825	0.91[EUR][1000 genomes]
rs1196831	0.91[EUR][1000 genomes]
rs1196833	0.91[EUR][1000 genomes]
rs1196839	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196841	0.91[EUR][1000 genomes]
rs1196842	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196844	0.91[EUR][1000 genomes]
rs1196848	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196851	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs1196852	1.00[CHB][hapmap]
rs1196853	0.92[EUR][1000 genomes]
rs1196859	0.89[EUR][1000 genomes]
rs1196861	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs1196862	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196864	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs1196869	0.90[EUR][1000 genomes]
rs1196871	0.88[EUR][1000 genomes]
rs1196872	0.89[EUR][1000 genomes]
rs1196873	0.90[EUR][1000 genomes]
rs1196874	0.91[EUR][1000 genomes]
rs1196881	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1196884	0.83[EUR][1000 genomes]
rs1206559	0.91[EUR][1000 genomes]
rs1209308	0.82[EUR][1000 genomes]
rs1209637	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1211276	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1211277	0.91[EUR][1000 genomes]
rs1211626	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12369709	0.88[EUR][1000 genomes]
rs12814458	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816560	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822081	1.00[CHB][hapmap]
rs1345096	0.81[EUR][1000 genomes]
rs1444610	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1621553	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1663564	1.00[CHB][hapmap]
rs1663565	0.89[EUR][1000 genomes]
rs1732370	0.91[EUR][1000 genomes]
rs2166142	0.81[EUR][1000 genomes]
rs2246243	0.83[EUR][1000 genomes]
rs2257156	0.91[EUR][1000 genomes]
rs2374449	0.80[EUR][1000 genomes]
rs2440692	0.81[EUR][1000 genomes]
rs2440714	0.86[EUR][1000 genomes]
rs2440715	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2440718	0.91[EUR][1000 genomes]
rs2464173	0.91[EUR][1000 genomes]
rs2464175	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs2464181	0.91[EUR][1000 genomes]
rs2464182	0.88[EUR][1000 genomes]
rs2888846	1.00[CHB][hapmap]
rs35679386	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356313	0.83[EUR][1000 genomes]
rs4372534	0.80[EUR][1000 genomes]
rs4390426	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs4545651	1.00[CHB][hapmap]
rs4964122	0.83[EUR][1000 genomes]
rs4964331	0.80[EUR][1000 genomes]
rs6539188	0.80[EUR][1000 genomes]
rs67604711	0.80[AMR][1000 genomes]
rs7132040	0.83[EUR][1000 genomes]
rs7132624	0.82[EUR][1000 genomes]
rs7132855	0.82[EUR][1000 genomes]
rs71441895	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299225	1.00[CHB][hapmap]
rs7302174	1.00[CHB][hapmap]
rs7303961	0.83[EUR][1000 genomes]
rs73181823	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959385	1.00[CHB][hapmap]
rs873119	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs935240	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs935241	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs935242	0.91[EUR][1000 genomes]
rs935244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935246	0.83[EUR][1000 genomes]
rs935248	0.92[EUR][1000 genomes]
rs935249	0.91[EUR][1000 genomes]
rs9645791	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1196777	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	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:105600800-105626800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:105605600-105628400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:105609200-105626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:105609200-105628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:105611200-105628200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:105611600-105626200	Weak transcription	Fetal Brain Male	brain
8	chr12:105616600-105629000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:105617000-105629000	Weak transcription	Esophagus	oesophagus
10	chr12:105617400-105629000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:105618600-105626800	Weak transcription	Gastric	stomach
12	chr12:105619400-105627400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:105620000-105625800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:105620400-105626000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:105620400-105626600	Weak transcription	Psoas Muscle	Psoas
16	chr12:105620600-105625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:105621200-105625800	Strong transcription	Primary B cells from cord blood	blood
18	chr12:105621200-105626200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:105621600-105627200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:105621800-105626400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:105621800-105626800	Enhancers	Brain Anterior Caudate	brain
22	chr12:105621800-105626800	Weak transcription	Fetal Kidney	kidney
23	chr12:105621800-105628600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:105621800-105628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:105622000-105627400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:105622000-105629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:105622400-105626800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:105622400-105628400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:105622600-105626800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr12:105622600-105627800	Weak transcription	HMEC	breast
31	chr12:105622800-105626800	Strong transcription	Primary T cells from cord blood	blood
32	chr12:105622800-105626800	Enhancers	Adipose Nuclei	Adipose
33	chr12:105622800-105628400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:105623000-105625600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:105623000-105625600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:105623000-105625800	Enhancers	HSMMtube	muscle
37	chr12:105623000-105626000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:105623000-105626200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:105623000-105626800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:105623000-105626800	Weak transcription	GM12878-XiMat	blood
41	chr12:105623000-105627600	Weak transcription	Thymus	Thymus
42	chr12:105623000-105627600	Weak transcription	Hela-S3	cervix
43	chr12:105623000-105628600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:105623200-105626600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:105623200-105626800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:105623200-105626800	Weak transcription	Liver	Liver
47	chr12:105623200-105627800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr12:105623200-105627800	Weak transcription	Fetal Thymus	thymus
49	chr12:105623200-105628000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr12:105623400-105626600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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