Variant report

Variant	rs3770455
Chromosome Location	chr2:172667895-172667896
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	CTCF	chr2:172667760-172667910	MCF-7	breast:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
2	RAD21	chr2:172667608-172668272	MCF-7	breast:	n/a	chr2:172667860-172667879 chr2:172667865-172667877
3	RAD21	chr2:172667706-172668027	A549	lung:	n/a	chr2:172667860-172667879 chr2:172667865-172667877
4	CTCF	chr2:172667820-172667970	HMEC	breast:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
5	CTCF	chr2:172667723-172667980	Medullo	brain:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
6	CTCF	chr2:172667780-172667930	HBMEC	blood vessel:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
7	CTCF	chr2:172667800-172667950	AG10803	skin:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
8	CTCF	chr2:172667775-172667970	Lung_OC	lung:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
9	CTCF	chr2:172667780-172667930	AG09319	gingival:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
10	CTCF	chr2:172667840-172667990	GM12873	blood:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
11	CTCF	chr2:172667666-172668082	IMR90	lung:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
12	CTCF	chr2:172667820-172667970	GM06990	blood:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
13	CTCF	chr2:172667780-172667930	NHDF-neo	bronchial:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
14	CTCF	chr2:172667605-172668097	A549	lung:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
15	CTCF	chr2:172667780-172667930	BJ	skin:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
16	CTCF	chr2:172667678-172668056	A549	lung:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
17	POLR2A	chr2:172667572-172668272	H1-neurons	neurons:	n/a	n/a
18	RAD21	chr2:172667697-172667984	K562	blood:	n/a	chr2:172667860-172667879 chr2:172667865-172667877
19	CUX1	chr2:172667672-172667996	K562	blood:	n/a	chr2:172667893-172667907
20	CTCF	chr2:172667748-172667983	Hela-S3	cervix:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
21	SMC3	chr2:172667622-172668585	SK-N-SH	brain:	n/a	chr2:172667861-172667875
22	CTCF	chr2:172667735-172667978	SK-N-SH_RA	brain:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
23	SMC3	chr2:172667695-172668045	K562	blood:	n/a	chr2:172667861-172667875
24	CTCF	chr2:172667880-172668030	BE2_C	brain:	n/a	n/a
25	CTCF	chr2:172667780-172667930	AG04450	lung:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
26	CTCF	chr2:172667880-172668030	HRPEpiC	eye:	n/a	n/a
27	CTCF	chr2:172667800-172667950	HEEpiC	esophagus:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
28	CTCF	chr2:172667758-172667951	LNCaP	prostate:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
29	CTCF	chr2:172667760-172667910	NHDF-neo	bronchial:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
30	CTCF	chr2:172667780-172667930	NB4	blood:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
31	CTCF	chr2:172667760-172667910	HVMF	connective:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
32	ATF1	chr2:172667707-172668101	K562	blood:	n/a	n/a
33	RAD21	chr2:172667715-172668065	K562	blood:	n/a	chr2:172667860-172667879 chr2:172667865-172667877
34	CTCF	chr2:172667634-172668123	K562	blood:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
35	RAD21	chr2:172667605-172668265	HCT-116	colon:	n/a	chr2:172667860-172667879 chr2:172667865-172667877
36	RAD21	chr2:172667681-172668164	A549	lung:	n/a	chr2:172667860-172667879 chr2:172667865-172667877
37	CTCF	chr2:172667311-172668299	A549	lung:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
38	CTCF	chr2:172667780-172667930	GM12872	blood:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
39	CTCF	chr2:172667760-172667910	GM12865	blood:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
40	CTCF	chr2:172667760-172667910	AoAF	blood vessel:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
41	RAD21	chr2:172667592-172668078	H1-hESC	embryonic stem cell:	n/a	chr2:172667860-172667879 chr2:172667865-172667877
42	RAD21	chr2:172667600-172668145	ECC-1	luminal epithelium:	n/a	chr2:172667860-172667879 chr2:172667865-172667877
43	CTCF	chr2:172667737-172667944	MCF-7	breast:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
44	CTCF	chr2:172667780-172667930	HEK293	kidney:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
45	ARID3A	chr2:172667674-172668055	K562	blood:	n/a	n/a
46	CTCF	chr2:172667860-172668010	WI-38	lung:	n/a	chr2:172667861-172667882
47	RFX5	chr2:172667732-172668040	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr2:172667760-172667910	HPF	lung:	n/a	chr2:172667859-172667877 chr2:172667861-172667882
49	CTCF	chr2:172667880-172668030	MCF-7	breast:	n/a	n/a
50	CTCF	chr2:172667780-172667930	SK-N-SH_RA	brain:	n/a	chr2:172667859-172667877 chr2:172667861-172667882

No.	Distal block	Cell Line	Cell type
1	chr2:172667340..172671964-chr2:172965434..172969900,7	MCF-7	breast:
2	chr2:172667394..172668045-chr2:172968332..172969197,4	MCF-7	breast:
3	chr2:172667374..172668555-chr2:172968288..172969185,6	K562	blood:
4	chr2:172667824..172668386-chr2:172970654..172971571,2	K562	blood:
5	chr2:172667609..172668156-chr2:172968074..172968614,2	MCF-7	breast:
6	chr2:172667461..172668379-chr2:172991701..172992562,2	K562	blood:
7	chr2:172667293..172668310-chr2:172971026..172971578,3	MCF-7	breast:
8	chr2:172666865..172669290-chr2:172948316..172950744,2	MCF-7	breast:

Variant related genes	Relation type
SLC25A12	TF binding region
ENSG00000144355	Chromatin interaction
ENSG00000236651	Chromatin interaction
ENSG00000115844	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12053046	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614709	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12619041	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12620126	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622385	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12622772	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12622895	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12624292	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs17428076	0.95[CEU][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs17581361	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17581439	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17581481	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs17581509	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs17615262	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17615352	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2176465	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3736499	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3765166	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3765167	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770448	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770449	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821093	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55864623	0.84[EUR][1000 genomes]
rs55957712	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56275355	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57718990	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57775770	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62182370	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62182372	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182373	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62182374	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62182392	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72881938	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72885532	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72885545	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72889848	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7584258	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3770455	BBS5	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172603000-172688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:172640400-172668000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:172642400-172688400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:172643600-172687800	Weak transcription	Hela-S3	cervix
5	chr2:172643800-172674600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:172644400-172681800	Weak transcription	Brain Substantia Nigra	brain
7	chr2:172644400-172684400	Weak transcription	Spleen	Spleen
8	chr2:172644600-172681800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:172645400-172687200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:172648200-172684400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:172648200-172687400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:172648200-172687400	Weak transcription	Colonic Mucosa	Colon
13	chr2:172648400-172671000	Weak transcription	Psoas Muscle	Psoas
14	chr2:172648400-172671200	Weak transcription	Right Ventricle	heart
15	chr2:172648400-172681800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:172648400-172687600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:172648800-172687400	Weak transcription	Esophagus	oesophagus
18	chr2:172649000-172687400	Weak transcription	Gastric	stomach
19	chr2:172649200-172682000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:172650400-172671200	Weak transcription	Adipose Nuclei	Adipose
21	chr2:172650400-172671400	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:172650400-172680200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:172650400-172681800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:172650400-172687400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:172650400-172687600	Weak transcription	Lung	lung
26	chr2:172650600-172669800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:172651800-172682000	Weak transcription	Fetal Thymus	thymus
28	chr2:172653000-172687400	Weak transcription	Fetal Heart	heart
29	chr2:172655200-172681800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:172655400-172687400	Weak transcription	A549	lung
31	chr2:172655600-172669800	Weak transcription	HSMMtube	muscle
32	chr2:172655600-172674600	Weak transcription	HSMM	muscle
33	chr2:172655600-172681800	Weak transcription	NHDF-Ad	bronchial
34	chr2:172655600-172687400	Weak transcription	NH-A	brain
35	chr2:172655800-172687400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:172656000-172679600	Weak transcription	Osteobl	bone
37	chr2:172656200-172683800	Weak transcription	Thymus	Thymus
38	chr2:172656400-172669600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:172656400-172682000	Weak transcription	Brain Anterior Caudate	brain
40	chr2:172656400-172684200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:172656400-172684400	Weak transcription	Aorta	Aorta
42	chr2:172657600-172687400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:172661200-172670000	Strong transcription	Primary T cells from cord blood	blood
44	chr2:172661600-172669000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:172662600-172682000	Weak transcription	Brain Hippocampus Middle	brain
46	chr2:172662800-172669600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:172663000-172669800	Weak transcription	Ovary	ovary
48	chr2:172663000-172682600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:172663600-172687400	Weak transcription	Fetal Brain Male	brain
50	chr2:172664000-172674800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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