Variant report

Variant	rs1196785
Chromosome Location	chr12:105629865-105629866
allele	C/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	POLR2A	chr12:105629745-105630400	GM12892	blood:	n/a	n/a
2	RFX5	chr12:105629672-105630314	Hela-S3	cervix:	n/a	chr12:105630121-105630136
3	MXI1	chr12:105629219-105630324	GM12878	blood:	n/a	chr12:105630122-105630137
4	ELF1	chr12:105629815-105630301	HepG2	liver:	n/a	chr12:105630014-105630025 chr12:105630015-105630024 chr12:105630014-105630025 chr12:105630065-105630074 chr12:105629983-105629996
5	POLR2A	chr12:105629399-105630256	A549	lung:	n/a	n/a
6	GABPA	chr12:105629421-105630242	HepG2	liver:	n/a	chr12:105629568-105629577
7	SMARCB1	chr12:105629049-105630289	Hela-S3	cervix:	n/a	n/a
8	MAZ	chr12:105629446-105630298	GM12878	blood:	n/a	chr12:105629576-105629586 chr12:105629573-105629583
9	POLR2A	chr12:105629641-105630331	K562	blood:	n/a	n/a
10	POLR2A	chr12:105629587-105630253	HepG2	liver:	n/a	n/a
11	TAF1	chr12:105629578-105630196	K562	blood:	n/a	n/a
12	POLR2A	chr12:105629442-105630391	HUVEC	blood vessel:	n/a	n/a
13	YY1	chr12:105629640-105630234	ECC-1	luminal epithelium:	n/a	chr12:105630072-105630086 chr12:105629844-105629855
14	MAX	chr12:105629626-105630509	Hela-S3	cervix:	n/a	n/a
15	MAX	chr12:105629552-105630249	H1-hESC	embryonic stem cell:	n/a	chr12:105629576-105629586 chr12:105629573-105629583
16	POLR2A	chr12:105629658-105630244	GM12891	blood:	n/a	n/a
17	YY1	chr12:105629836-105630268	GM12891	blood:	n/a	chr12:105630072-105630086 chr12:105629844-105629855
18	POLR2A	chr12:105629455-105630266	A549	lung:	n/a	n/a
19	TCF12	chr12:105629836-105630649	A549	lung:	n/a	n/a
20	ETS1	chr12:105629822-105630269	GM12878	blood:	n/a	chr12:105630063-105630074 chr12:105630016-105630025 chr12:105630012-105630028 chr12:105630046-105630055 chr12:105630016-105630025 chr12:105630014-105630023 chr12:105630016-105630027 chr12:105630046-105630055 chr12:105630016-105630025 chr12:105629987-105630001 chr12:105630046-105630055 chr12:105630042-105630058 chr12:105629987-105629996 chr12:105630016-105630025 chr12:105630046-105630055 chr12:105630015-105630024 chr12:105630016-105630025 chr12:105630016-105630025 chr12:105630016-105630025 chr12:105630046-105630055
21	POLR2A	chr12:105629461-105630467	HepG2	liver:	n/a	n/a
22	POLR2A	chr12:105629497-105630325	K562	blood:	n/a	n/a
23	YY1	chr12:105629368-105630234	HepG2	liver:	n/a	chr12:105629513-105629522 chr12:105630072-105630086 chr12:105629844-105629855
24	POLR2A	chr12:105629515-105630566	Hela-S3	cervix:	n/a	n/a
25	HEY1	chr12:105629598-105630291	K562	blood:	n/a	chr12:105630090-105630105
26	RAD21	chr12:105629016-105630689	IMR90	lung:	n/a	chr12:105629805-105629818
27	RCOR1	chr12:105629161-105630515	K562	blood:	n/a	n/a
28	BCL3	chr12:105629823-105630623	A549	lung:	n/a	chr12:105630016-105630025 chr12:105629987-105629996
29	POLR2A	chr12:105628893-105630852	SK-N-SH	brain:	n/a	n/a
30	MAZ	chr12:105629344-105630237	HepG2	liver:	n/a	chr12:105629576-105629586 chr12:105629573-105629583
31	ETS1	chr12:105629734-105630134	K562	blood:	n/a	chr12:105630063-105630074 chr12:105630016-105630025 chr12:105630012-105630028 chr12:105630046-105630055 chr12:105630016-105630025 chr12:105630014-105630023 chr12:105630016-105630027 chr12:105630046-105630055 chr12:105630016-105630025 chr12:105629987-105630001 chr12:105630046-105630055 chr12:105630042-105630058 chr12:105629987-105629996 chr12:105630016-105630025 chr12:105630046-105630055 chr12:105630015-105630024 chr12:105630016-105630025 chr12:105630016-105630025 chr12:105630016-105630025 chr12:105630046-105630055
32	MAX	chr12:105629644-105630453	ECC-1	luminal epithelium:	n/a	n/a
33	TAF1	chr12:105629506-105630202	HepG2	liver:	n/a	n/a
34	GABPA	chr12:105629351-105630429	K562	blood:	n/a	chr12:105629568-105629577
35	MXI1	chr12:105629126-105630304	HepG2	liver:	n/a	chr12:105630122-105630137
36	YY1	chr12:105629439-105630178	K562	blood:	n/a	chr12:105629513-105629522 chr12:105630072-105630086 chr12:105629844-105629855
37	YY1	chr12:105629493-105630286	GM12878	blood:	n/a	chr12:105629513-105629522 chr12:105630072-105630086 chr12:105629844-105629855
38	TAF1	chr12:105629666-105630416	A549	lung:	n/a	n/a
39	GABPA	chr12:105629846-105630214	GM12878	blood:	n/a	n/a
40	YY1	chr12:105629514-105630227	SK-N-SH_RA	brain:	n/a	chr12:105630072-105630086 chr12:105629844-105629855
41	GABPA	chr12:105629730-105630407	HL-60	blood:	n/a	n/a
42	POLR2A	chr12:105629508-105630326	MCF-7	breast:	n/a	n/a
43	POLR2A	chr12:105629518-105630413	PFSK-1	brain:	n/a	n/a
44	GABPA	chr12:105629737-105630366	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr12:105629786-105630208	K562	blood:	n/a	n/a
46	POLR2A	chr12:105629539-105630328	HEK293	kidney:	n/a	n/a
47	EBF1	chr12:105629468-105629920	GM12878	blood:	n/a	n/a
48	CHD1	chr12:105629658-105630448	GM12878	blood:	n/a	chr12:105629705-105629715
49	ELF1	chr12:105629816-105630387	A549	lung:	n/a	chr12:105630014-105630025 chr12:105630015-105630024 chr12:105630014-105630025 chr12:105630065-105630074 chr12:105629983-105629996
50	ELF1	chr12:105629771-105630268	K562	blood:	n/a	chr12:105630014-105630025 chr12:105630015-105630024 chr12:105630014-105630025 chr12:105630065-105630074 chr12:105629983-105629996

No.	Distal block	Cell Line	Cell type
1	chr12:105629476..105630447-chr15:74753281..74753992,2	Hela-S3	cervix:
2	chr12:104682529..104684202-chr12:105629338..105630884,2	MCF-7	breast:
3	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:
4	chr12:105629495..105630048-chr20:30696905..30697754,2	Hela-S3	cervix:
5	chr12:105628750..105631438-chr12:105722608..105725285,3	MCF-7	breast:
6	chr12:105499144..105502991-chr12:105627617..105631044,5	MCF-7	breast:
7	chr12:105628899..105630525-chr15:65596241..65598833,2	MCF-7	breast:
8	chr12:105610784..105617210-chr12:105628529..105631630,8	MCF-7	breast:
9	chr12:105501540..105503183-chr12:105627693..105630661,2	MCF-7	breast:
10	chr12:8088360..8089072-chr12:105629548..105630374,2	Hela-S3	cervix:
11	chr1:23885024..23885849-chr12:105629853..105630565,2	Hela-S3	cervix:
12	chr12:105500023..105502355-chr12:105628064..105629909,2	K562	blood:
13	chr12:105500023..105504653-chr12:105628064..105630551,4	K562	blood:
14	chr12:105629542..105630454-chr19:18392234..18393176,2	Hela-S3	cervix:
15	chr12:105542946..105545712-chr12:105628511..105631314,2	MCF-7	breast:

Variant related genes	Relation type
APPL2	TF binding region
ENSG00000136044	Chromatin interaction
ENSG00000117318	Chromatin interaction
ENSG00000257999	Chromatin interaction
ENSG00000101337	Chromatin interaction
ENSG00000247240	Chromatin interaction
ENSG00000059804	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000138629	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10778374	0.81[ASN][1000 genomes]
rs10778375	0.85[ASN][1000 genomes]
rs1109432	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112436	0.86[ASN][1000 genomes]
rs1196750	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196766	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196767	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196768	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196776	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196778	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196779	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196781	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196788	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196804	0.84[EUR][1000 genomes]
rs1196809	0.84[EUR][1000 genomes]
rs1196814	0.84[EUR][1000 genomes]
rs1196822	0.83[EUR][1000 genomes]
rs1196835	0.83[EUR][1000 genomes]
rs1196836	0.83[EUR][1000 genomes]
rs1196838	0.81[EUR][1000 genomes]
rs1196854	0.86[EUR][1000 genomes]
rs1196856	0.86[EUR][1000 genomes]
rs1196860	0.83[EUR][1000 genomes]
rs1196866	0.86[EUR][1000 genomes]
rs1196867	0.84[EUR][1000 genomes]
rs1196868	0.86[EUR][1000 genomes]
rs1196878	0.83[EUR][1000 genomes]
rs1201657	0.86[EUR][1000 genomes]
rs1317941	0.87[ASN][1000 genomes]
rs17036869	0.85[ASN][1000 genomes]
rs1732378	0.86[EUR][1000 genomes]
rs1732379	0.86[EUR][1000 genomes]
rs2264066	0.86[EUR][1000 genomes]
rs2374448	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440708	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440717	0.84[EUR][1000 genomes]
rs4964127	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4964346	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6539196	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs727888	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309320	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310488	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969800	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]

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
rs1196785	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105627600-105630600	Active TSS	Aorta	Aorta
2	chr12:105628000-105630400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr12:105628000-105630600	Active TSS	Colonic Mucosa	Colon
4	chr12:105628200-105630400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:105628200-105630600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:105628200-105630800	Active TSS	GM12878-XiMat	blood
7	chr12:105628400-105630200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr12:105628400-105630200	Active TSS	NHLF	lung
9	chr12:105628400-105630400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr12:105628400-105630400	Active TSS	Brain Cingulate Gyrus	brain
11	chr12:105628400-105630400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:105628400-105630400	Active TSS	Fetal Intestine Large	intestine
13	chr12:105628400-105630400	Active TSS	Left Ventricle	heart
14	chr12:105628400-105630400	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr12:105628400-105630400	Active TSS	NHDF-Ad	bronchial
16	chr12:105628400-105630600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:105628400-105630600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:105628400-105630600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:105628400-105630600	Active TSS	Fetal Intestine Small	intestine
20	chr12:105628400-105630600	Active TSS	Psoas Muscle	Psoas
21	chr12:105628400-105630600	Active TSS	Right Atrium	heart
22	chr12:105628400-105630600	Active TSS	HSMMtube	muscle
23	chr12:105628600-105630200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr12:105628600-105630200	Active TSS	Brain Angular Gyrus	brain
25	chr12:105628600-105630200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr12:105628600-105630400	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr12:105628600-105630400	Active TSS	Thymus	Thymus
28	chr12:105628600-105630400	Active TSS	HSMM	muscle
29	chr12:105628600-105630600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:105628600-105630600	Active TSS	H1 Cell Line	embryonic stem cell
31	chr12:105628600-105630600	Active TSS	Ovary	ovary
32	chr12:105628600-105630600	Active TSS	Right Ventricle	heart
33	chr12:105628800-105630200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:105628800-105630200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:105628800-105630200	Active TSS	Brain Hippocampus Middle	brain
36	chr12:105628800-105630200	Active TSS	NH-A	brain
37	chr12:105628800-105630200	Active TSS	Osteobl	bone
38	chr12:105628800-105630400	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr12:105628800-105630400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:105628800-105630600	Active TSS	H9 Cell Line	embryonic stem cell
41	chr12:105628800-105630600	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr12:105628800-105630600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:105628800-105630800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr12:105628800-105630800	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr12:105628800-105630800	Active TSS	Stomach Smooth Muscle	stomach
46	chr12:105629000-105630200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:105629000-105630200	Active TSS	Muscle Satellite Cultured Cells	--
48	chr12:105629000-105630200	Active TSS	Gastric	stomach
49	chr12:105629000-105630200	Active TSS	A549	lung
50	chr12:105629000-105630200	Bivalent/Poised TSS	HepG2	liver

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