Variant report

Variant	rs3770696
Chromosome Location	chr2:211310200-211310201
allele	A/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	RAD21	chr2:211309894-211310233	H1-hESC	embryonic stem cell:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
2	RAD21	chr2:211309878-211310246	IMR90	lung:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
3	RAD21	chr2:211309788-211310310	A549	lung:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
4	RAD21	chr2:211309864-211310237	GM12878	blood:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
5	SMC3	chr2:211309927-211310243	K562	blood:	n/a	chr2:211310032-211310046
6	CTCF	chr2:211309917-211310235	K562	blood:	n/a	chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053 chr2:211310034-211310041
7	CTCF	chr2:211309871-211310256	HepG2	liver:	n/a	chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053 chr2:211310034-211310041
8	CTCF	chr2:211309880-211310203	HUVEC	blood vessel:	n/a	chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053 chr2:211310034-211310041
9	RAD21	chr2:211309864-211310319	HCT-116	colon:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
10	ARID3A	chr2:211309814-211310221	K562	blood:	n/a	n/a
11	CTCF	chr2:211309697-211310367	A549	lung:	n/a	chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053 chr2:211310034-211310041
12	ZNF143	chr2:211309876-211310209	GM12878	blood:	n/a	n/a
13	RAD21	chr2:211309855-211310246	Hela-S3	cervix:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
14	CTCF	chr2:211309804-211310255	A549	lung:	n/a	chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053 chr2:211310034-211310041
15	CTCF	chr2:211309774-211310290	HCT-116	colon:	n/a	chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053 chr2:211310034-211310041
16	RAD21	chr2:211309872-211310237	HepG2	liver:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
17	SMC3	chr2:211309895-211310227	Hela-S3	cervix:	n/a	chr2:211310032-211310046
18	RAD21	chr2:211309840-211310234	SK-N-SH_RA	brain:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
19	SMC3	chr2:211309864-211310228	GM12878	blood:	n/a	chr2:211310032-211310046
20	RFX5	chr2:211309651-211310265	SK-N-SH	brain:	n/a	chr2:211310242-211310250
21	RAD21	chr2:211309899-211310278	ECC-1	luminal epithelium:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
22	RAD21	chr2:211309899-211310313	HCT-116	colon:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
23	RAD21	chr2:211309907-211310297	MCF-7	breast:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
24	CTCF	chr2:211309632-211310488	SK-N-SH	brain:	n/a	chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053 chr2:211310034-211310041
25	CTCF	chr2:211309831-211310238	IMR90	lung:	n/a	chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053 chr2:211310034-211310041
26	RAD21	chr2:211309782-211310316	HepG2	liver:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
27	CTCF	chr2:211309833-211310252	GM12878	blood:	n/a	chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053 chr2:211310034-211310041
28	MAFK	chr2:211309862-211310214	IMR90	lung:	n/a	chr2:211310008-211310025
29	CTCF	chr2:211309905-211310300	MCF-7	breast:	n/a	chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053 chr2:211310034-211310041
30	CTCF	chr2:211309839-211310227	K562	blood:	n/a	chr2:211310034-211310041 chr2:211310031-211310047 chr2:211310030-211310048 chr2:211310032-211310053
31	RAD21	chr2:211309771-211310473	SK-N-SH	brain:	n/a	chr2:211310031-211310050 chr2:211310032-211310041
32	CUX1	chr2:211309848-211310209	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:211309754..211310533-chr2:211481854..211482775,2	MCF-7	breast:

Variant related genes	Relation type
LANCL1	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10184506	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10195425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10515951	0.88[TSI][hapmap]
rs10932340	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs12694198	0.93[ASN][1000 genomes]
rs13005638	0.83[EUR][1000 genomes]
rs13013076	0.85[CEU][hapmap]
rs13420747	0.85[JPT][hapmap]
rs1509816	1.00[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1858194	0.82[EUR][1000 genomes]
rs1858195	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2160851	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs2287426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2287427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2370962	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs2664239	1.00[CEU][hapmap]
rs34374637	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35003355	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732058	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755185	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755186	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770686	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770688	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3845634	0.87[CEU][hapmap]
rs4640325	0.88[TSI][hapmap]
rs4672580	0.83[EUR][1000 genomes]
rs4672581	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4672582	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6749711	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7590759	1.00[CEU][hapmap]
rs759688	1.00[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs759689	0.88[AMR][1000 genomes]
rs918234	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs9941507	1.00[CEU][hapmap];0.88[TSI][hapmap]

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	nsv1012567	chr2:211087588-211315554	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv875767	chr2:211119233-211334647	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv3147	chr2:211281479-211326844	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3770696	LANCL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211292400-211323000	Weak transcription	Fetal Brain Male	brain
2	chr2:211293200-211311600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:211293800-211335400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:211294800-211322200	Weak transcription	K562	blood
5	chr2:211294800-211333200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:211295000-211330400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:211295000-211336000	Weak transcription	Colonic Mucosa	Colon
8	chr2:211295000-211340600	Weak transcription	HUVEC	blood vessel
9	chr2:211296000-211340200	Weak transcription	Small Intestine	intestine
10	chr2:211296400-211341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:211297400-211321400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:211297800-211336200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:211299400-211322600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:211299600-211322400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:211299800-211318600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:211299800-211330000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:211300200-211326000	Weak transcription	NHDF-Ad	bronchial
18	chr2:211300400-211329800	Weak transcription	A549	lung
19	chr2:211301200-211317000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr2:211301200-211319200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:211301200-211319200	Weak transcription	Fetal Stomach	stomach
22	chr2:211301200-211322400	Weak transcription	Aorta	Aorta
23	chr2:211301200-211322600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:211301200-211322600	Weak transcription	Pancreas	Pancrea
25	chr2:211301200-211322600	Weak transcription	Spleen	Spleen
26	chr2:211301200-211325400	Weak transcription	Esophagus	oesophagus
27	chr2:211301200-211330000	Weak transcription	Gastric	stomach
28	chr2:211301200-211340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:211301200-211340600	Weak transcription	Fetal Intestine Small	intestine
30	chr2:211301200-211340800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:211301400-211311000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:211301400-211318800	Weak transcription	Psoas Muscle	Psoas
33	chr2:211301400-211319000	Weak transcription	Fetal Kidney	kidney
34	chr2:211301400-211319200	Weak transcription	Thymus	Thymus
35	chr2:211301400-211330000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:211301400-211330800	Weak transcription	Right Ventricle	heart
37	chr2:211301400-211334400	Weak transcription	NHEK	skin
38	chr2:211301400-211336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:211301800-211315800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:211301800-211318000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:211302200-211311400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:211302200-211319200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:211302600-211318400	Weak transcription	HMEC	breast
44	chr2:211302600-211319000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:211303000-211316600	Weak transcription	Placenta	Placenta
46	chr2:211303600-211319200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:211303800-211319000	Weak transcription	NHLF	lung
48	chr2:211304200-211315800	Weak transcription	HSMM	muscle
49	chr2:211304200-211319400	Weak transcription	Hela-S3	cervix
50	chr2:211305200-211311400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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