Variant report

Variant	rs35911561
Chromosome Location	chr3:52722562-52722563
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:52722235-52722799	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:52721385-52732213	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:52718446-52723739	IMR90	lung:	n/a	n/a
4	GATA3	chr3:52722099-52722768	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:52719170-52723469	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:52718374-52724293	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:52722144-52723209	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr3:52719148-52723512	GM12878	blood:	n/a	n/a
9	GATA3	chr3:52722281-52722714	T-47D	breast:	n/a	n/a
10	POLR2A	chr3:52722543-52722725	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:52722290-52723450	GM12892	blood:	n/a	n/a
12	POLR2A	chr3:52722488-52723585	K562	blood:	n/a	n/a
13	POLR2A	chr3:52721500-52723097	A549	lung:	n/a	n/a
14	POLR2A	chr3:52722426-52724355	GM12892	blood:	n/a	n/a
15	POLR2A	chr3:52719158-52723679	GM12891	blood:	n/a	n/a
16	CEBPB	chr3:52722246-52722743	MCF-7	breast:	n/a	chr3:52722596-52722609 chr3:52722353-52722364
17	POLR2A	chr3:52722367-52722763	GM12891	blood:	n/a	n/a
18	POLR2A	chr3:52721824-52723582	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:52722477-52723538	GM12891	blood:	n/a	n/a
20	POLR2A	chr3:52722527-52723189	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:52722551-52723358	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:52721777-52723421	GM12878	blood:	n/a	n/a
23	NR2F2	chr3:52722353-52722811	MCF-7	breast:	n/a	n/a
24	CEBPB	chr3:52722178-52722847	MCF-7	breast:	n/a	chr3:52722596-52722609 chr3:52722353-52722364
25	POLR2A	chr3:52719176-52724220	GM12892	blood:	n/a	n/a
26	SIN3AK20	chr3:52722197-52722834	MCF-7	breast:	n/a	n/a
27	SIN3AK20	chr3:52722282-52722722	MCF-7	breast:	n/a	n/a
28	POLR2A	chr3:52721197-52724243	GM12892	blood:	n/a	n/a
29	POLR2A	chr3:52722145-52723451	GM12891	blood:	n/a	n/a
30	POLR2A	chr3:52722488-52723173	H1-hESC	embryonic stem cell:	n/a	n/a
31	FOXA1	chr3:52722332-52722683	T-47D	breast:	n/a	n/a
32	POLR2A	chr3:52721204-52724270	SK-N-MC	brain:	n/a	n/a
33	FOXA1	chr3:52722280-52722682	T-47D	breast:	n/a	n/a
34	POLR2A	chr3:52722445-52723645	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:52719175-52724181	MCF10A-Er-Src	breast:	n/a	n/a
36	GATA3	chr3:52722234-52722736	T-47D	breast:	n/a	n/a
37	POLR2A	chr3:52719170-52723594	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:52722534-52723474	K562	blood:	n/a	n/a
39	ZNF263	chr3:52722295-52722739	HEK293-T-REx	kidney:	n/a	chr3:52722406-52722427

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52719561..52722875-chr3:52731308..52733675,5	MCF-7	breast:
2	chr3:52487997..52491865-chr3:52718755..52722667,5	MCF-7	breast:
3	chr3:52567779..52572340-chr3:52718708..52722750,6	K562	blood:
4	chr3:52718628..52724105-chr3:52738117..52743946,12	MCF-7	breast:
5	chr3:52722327..52724239-chr3:52736017..52737840,2	MCF-7	breast:
6	chr3:52718708..52722190-chr3:52722401..52727615,8	MCF-7	breast:
7	chr3:52719608..52722839-chr3:52830545..52833712,3	K562	blood:

No data

Variant related genes	Relation type
SNORD19	TF binding region
PBRM1	TF binding region
ENSG00000222345	TF binding region
GNL3	TF binding region
SNORD19B	TF binding region
SNORD69	TF binding region
ENSG00000252787	TF binding region
ENSG00000114854	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000162267	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000163939	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10510759	0.94[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs12107484	0.94[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs13063138	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13086936	0.91[CEU][hapmap];1.00[CHD][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087538	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13099479	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34131802	0.82[ASN][1000 genomes]
rs34182518	0.91[CEU][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34735556	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35198201	1.00[ASN][1000 genomes]
rs35225119	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35272104	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs45556336	0.82[ASN][1000 genomes]
rs4687545	0.90[CEU][hapmap]
rs56156188	0.87[AFR][1000 genomes]
rs57008939	0.87[AFR][1000 genomes]
rs61220667	0.86[AFR][1000 genomes]
rs6780005	0.95[YRI][hapmap]
rs71299610	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299613	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299614	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72950430	0.84[AFR][1000 genomes]
rs72950432	0.82[AFR][1000 genomes]
rs7614424	0.91[CEU][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]

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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs35911561	ITIH3	cis	parietal	SCAN
rs35911561	GNL3	cis	Skin Sun Exposed Lower leg	GTEx
rs35911561	TMEM110	cis	parietal	SCAN
rs35911561	TMEM110	cis	cerebellum	SCAN
rs35911561	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52720600-52722600	Transcr. at gene 5' and 3'	A549	lung
2	chr3:52720600-52723200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
3	chr3:52720800-52722800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:52721000-52722600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:52721000-52722800	Transcr. at gene 5' and 3'	Hela-S3	cervix
6	chr3:52721000-52723600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
7	chr3:52721000-52728000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:52721000-52730400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:52721000-52734400	Strong transcription	Fetal Stomach	stomach
10	chr3:52721000-52738600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:52721200-52722600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:52721200-52722600	Genic enhancers	Liver	Liver
13	chr3:52721200-52722800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr3:52721200-52722800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:52721200-52722800	Genic enhancers	Rectal Mucosa Donor 31	rectum
16	chr3:52721200-52723400	Genic enhancers	Stomach Mucosa	stomach
17	chr3:52721200-52730600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:52721200-52731600	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr3:52721200-52732200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:52721200-52732200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:52721200-52732200	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:52721200-52733000	Strong transcription	Stomach Smooth Muscle	stomach
23	chr3:52721200-52734400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:52721400-52722600	Weak transcription	Fetal Heart	heart
25	chr3:52721400-52722600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
26	chr3:52721400-52722800	Genic enhancers	Fetal Intestine Large	intestine
27	chr3:52721400-52722800	Genic enhancers	Fetal Intestine Small	intestine
28	chr3:52721400-52725400	Strong transcription	Rectal Smooth Muscle	rectum
29	chr3:52721400-52730800	Strong transcription	Lung	lung
30	chr3:52721400-52731800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:52721400-52732000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:52721400-52732200	Strong transcription	Brain Angular Gyrus	brain
33	chr3:52721400-52732200	Strong transcription	Colon Smooth Muscle	Colon
34	chr3:52721400-52732400	Strong transcription	Brain Anterior Caudate	brain
35	chr3:52721400-52732400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:52721400-52732800	Strong transcription	Fetal Brain Female	brain
37	chr3:52721400-52732800	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:52721400-52733000	Strong transcription	Adipose Nuclei	Adipose
39	chr3:52721400-52734000	Strong transcription	Primary B cells from cord blood	blood
40	chr3:52721400-52734200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:52721400-52734400	Strong transcription	Brain Hippocampus Middle	brain
42	chr3:52721400-52734400	Strong transcription	Fetal Lung	lung
43	chr3:52721400-52734400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:52721400-52734600	Strong transcription	Primary T cells from cord blood	blood
45	chr3:52721400-52735800	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:52721600-52722600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:52721600-52722600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:52721600-52722600	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr3:52721600-52722600	Genic enhancers	HMEC	breast
50	chr3:52721600-52722800	Genic enhancers	Pancreas	Pancrea

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