Variant report

Variant	rs3754750
Chromosome Location	chr2:173887053-173887054
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	CTCF	chr2:173886486-173887145	HCT-116	colon:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
2	RAD21	chr2:173886518-173887090	A549	lung:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
3	CTCF	chr2:173886166-173887245	A549	lung:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
4	CTCF	chr2:173887040-173887190	HPF	lung:	n/a	n/a
5	CTCF	chr2:173886518-173887144	MCF-7	breast:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
6	RAD21	chr2:173886560-173887061	H1-hESC	embryonic stem cell:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
7	CTCF	chr2:173887020-173887170	K562	blood:	n/a	n/a
8	CTCF	chr2:173886960-173887110	HRPEpiC	eye:	n/a	n/a
9	CTCF	chr2:173887020-173887170	AG04449	skin:	n/a	n/a
10	CTCF	chr2:173886920-173887070	GM12872	blood:	n/a	n/a
11	SP1	chr2:173886531-173887078	A549	lung:	n/a	n/a
12	TCF12	chr2:173886477-173887117	A549	lung:	n/a	n/a
13	RAD21	chr2:173886428-173887096	A549	lung:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
14	CEBPB	chr2:173886495-173887064	A549	lung:	n/a	chr2:173886748-173886759 chr2:173886748-173886761
15	CTCF	chr2:173887000-173887150	SK-N-SH_RA	brain:	n/a	n/a
16	RAD21	chr2:173886462-173887062	HCT-116	colon:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
17	CTCF	chr2:173886453-173887171	SK-N-SH	brain:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
18	CTCF	chr2:173886497-173887075	MCF-7	breast:	n/a	chr2:173886800-173886813 chr2:173886793-173886814 chr2:173886798-173886816
19	RAD21	chr2:173886467-173887267	SK-N-SH	brain:	n/a	chr2:173886796-173886815 chr2:173886799-173886812
20	CTCF	chr2:173886920-173887070	GM12864	blood:	n/a	n/a
21	SMC3	chr2:173886611-173887089	SK-N-SH	brain:	n/a	chr2:173886800-173886814

No.	Distal block	Cell Line	Cell type
1	chr2:173841835..173842797-chr2:173886338..173887289,8	MCF-7	breast:
2	chr2:173840817..173843158-chr2:173885041..173887379,4	MCF-7	breast:
3	chr2:173729672..173730467-chr2:173886391..173887246,2	MCF-7	breast:
4	chr2:173885808..173888407-chr2:173907815..173910951,3	MCF-7	breast:
5	chr2:173860750..173861295-chr2:173886636..173887202,2	MCF-7	breast:
6	chr2:173841773..173843105-chr2:173886256..173887211,13	MCF-7	breast:
7	chr2:173867155..173868911-chr2:173885451..173888088,2	MCF-7	breast:
8	chr2:173836656..173837372-chr2:173886327..173887177,4	MCF-7	breast:
9	chr2:173670836..173671405-chr2:173886290..173887243,2	MCF-7	breast:
10	chr2:173885113..173887445-chr2:173889594..173892152,2	K562	blood:
11	chr2:173887008..173888780-chr2:173890982..173893784,2	MCF-7	breast:
12	chr2:173846019..173848383-chr2:173886848..173888361,2	MCF-7	breast:
13	chr2:173836694..173837365-chr2:173886317..173887226,2	K562	blood:

Variant related genes	Relation type
RAPGEF4	TF binding region
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2305462	0.87[GIH][hapmap];0.88[JPT][hapmap]
rs3754751	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3769219	0.86[JPT][hapmap]
rs3769220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3769222	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs3769224	1.00[ASN][1000 genomes]
rs3820839	0.88[JPT][hapmap]
rs729486	0.88[JPT][hapmap]
rs7595061	1.00[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	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3754750	PPIG	cis	parietal	SCAN
rs3754750	ZAK	cis	cerebellum	SCAN
rs3754750	SCRN3	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173856200-173892600	Weak transcription	Brain Angular Gyrus	brain
2	chr2:173861000-173888000	Weak transcription	Fetal Stomach	stomach
3	chr2:173868000-173902000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:173868600-173892200	Weak transcription	Fetal Intestine Large	intestine
5	chr2:173877200-173901600	Weak transcription	Gastric	stomach
6	chr2:173877800-173887800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:173879400-173888600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:173880800-173891600	Strong transcription	Liver	Liver
9	chr2:173881200-173892400	Weak transcription	Fetal Intestine Small	intestine
10	chr2:173881200-173912800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:173881400-173887200	Weak transcription	Esophagus	oesophagus
12	chr2:173881400-173897200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:173883000-173892200	Weak transcription	Right Atrium	heart
14	chr2:173884800-173893000	Weak transcription	Right Ventricle	heart
15	chr2:173885400-173890800	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:173885400-173892000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:173885400-173892600	Weak transcription	Brain Anterior Caudate	brain
18	chr2:173886000-173888000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:173886200-173887800	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:173886200-173890000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:173886400-173887200	Enhancers	Hela-S3	cervix
22	chr2:173886400-173887400	Enhancers	Fetal Heart	heart
23	chr2:173886600-173887200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:173886800-173887200	Enhancers	Adipose Nuclei	Adipose
25	chr2:173886800-173887200	Enhancers	Psoas Muscle	Psoas
26	chr2:173886800-173887200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:173886800-173887400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:173886800-173888200	Strong transcription	Lung	lung
29	chr2:173886800-173888600	Strong transcription	Ovary	ovary
30	chr2:173886800-173890600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:173887000-173887200	Enhancers	Left Ventricle	heart
32	chr2:173887000-173887200	Enhancers	A549	lung
33	chr2:173887000-173887400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:173887000-173890000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:173887000-173891400	Weak transcription	Fetal Lung	lung

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