Variant report

Variant	rs3099952
Chromosome Location	chr2:39004215-39004216
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:39004204-39004254	RPTEC	kidney:	n/a
2	chr2:39004204-39004254	ECC-1	luminal epithelium:	n/a
3	chr2:39004204-39004254	HIPEpiC	eye:	n/a
4	chr2:39004204-39004254	Hela-S3	cervix:	n/a
5	chr2:39004204-39004254	T-47D	breast:	n/a
6	chr2:39004204-39004254	HL-60	blood:	n/a
7	chr2:39004204-39004254	BE2_C	brain:	n/a
8	chr2:39004204-39004254	PrEC	prostate:	n/a
9	chr2:39004204-39004254	IMR90	lung:	fetal
10	chr2:39004204-39004254	HEEpiC	esophagus:	n/a
11	chr2:39004204-39004254	SK-N-MC	brain:	n/a
12	chr2:39004204-39004254	HRCEpiC	kidney:	n/a
13	chr2:39004204-39004254	NT2-D1	testis:	n/a
14	chr2:39004204-39004254	NHDF-neo	bronchial:	n/a
15	chr2:39004204-39004254	HEK293	kidney:	embryo
16	chr2:39004204-39004254	SKMC	muscle:	n/a
17	chr2:39004204-39004254	AoSMC	blood vessel:	n/a
18	chr2:39004204-39004254	PANC-1	pancreas:	n/a
19	chr2:39004204-39004254	ovcar-3	ovarian:	n/a
20	chr2:39004204-39004254	HMEC	breast:	n/a
21	chr2:39004204-39004254	HCT-116	colon:	n/a
22	chr2:39004204-39004254	HUVEC	blood vessel:	n/a
23	chr2:39004204-39004254	AG10803	skin:	n/a
24	chr2:39004204-39004254	MCF-7	breast:	n/a
25	chr2:39004204-39004254	GM12891	blood:	n/a
26	chr2:39004204-39004254	ProgFib	skin:	n/a
27	chr2:39004204-39004254	HPAEpiC	pulmonary alveolar:	n/a
28	chr2:39004204-39004254	SK-N-SH_RA	brain:	n/a
29	chr2:39004204-39004254	MCF10A-Er-Src	breast:	n/a
30	chr2:39004204-39004254	HRPEpiC	eye:	n/a
31	chr2:39004204-39004254	K562	blood:	n/a
32	chr2:39004204-39004254	A549	lung:	n/a
33	chr2:39004204-39004254	Jurkat	blood:	n/a
34	chr2:39004204-39004254	HAEpiC	amniotic membrane:	n/a
35	chr2:39004204-39004254	HepG2	liver:	n/a
36	chr2:39004204-39004254	GM12892	blood:	n/a
37	chr2:39004204-39004254	AG04449	skin:	fetal
38	chr2:39004204-39004254	HCPEpiC	choroid plexus:	n/a
39	chr2:39004204-39004254	NB4	blood:	n/a
40	chr2:39004204-39004254	GM06990	blood:	n/a
41	chr2:39004204-39004254	H1-hESC	embryonic stem cell:	embryo
42	chr2:39004204-39004254	CMK	blood:	n/a
43	chr2:39004204-39004254	AG09309	skin:	n/a
44	chr2:39004204-39004254	HRE	kidney:	n/a
45	chr2:39004204-39004254	NH-A	brain:	n/a
46	chr2:39004204-39004254	SAEC	small airway:	n/a
47	chr2:39004204-39004254	HNPCEpiC	eye:	n/a
48	chr2:39004204-39004254	SK-N-SH	brain:	n/a
49	chr2:39004204-39004254	AG09319	gingival:	n/a
50	chr2:39004204-39004254	GM12878	blood:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
2	chr2:38975156..38979928-chr2:39002986..39007194,11	MCF-7	breast:
3	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
4	chr2:38976218..38980921-chr2:39003670..39007764,15	K562	blood:
5	chr2:38983494..38986054-chr2:39002724..39005182,2	K562	blood:

No data

Variant related genes	Relation type
GEMIN6	CpG island
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10173118	0.88[ASN][1000 genomes]
rs11694383	1.00[ASN][1000 genomes]
rs11889280	0.91[ASN][1000 genomes]
rs12465043	0.83[ASN][1000 genomes]
rs12468732	0.83[ASN][1000 genomes]
rs12469681	0.88[ASN][1000 genomes]
rs12473036	0.88[ASN][1000 genomes]
rs12474770	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12477252	0.88[ASN][1000 genomes]
rs12621103	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12712621	0.81[ASN][1000 genomes]
rs12996194	0.84[ASN][1000 genomes]
rs13011522	0.83[ASN][1000 genomes]
rs13014136	0.88[ASN][1000 genomes]
rs13024811	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13029406	0.85[ASN][1000 genomes]
rs13383541	0.82[ASN][1000 genomes]
rs13411868	0.88[ASN][1000 genomes]
rs13417196	0.88[ASN][1000 genomes]
rs1530852	0.85[ASN][1000 genomes]
rs1530853	0.85[ASN][1000 genomes]
rs1979142	0.80[ASN][1000 genomes]
rs3099960	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099961	0.87[AMR][1000 genomes]
rs3099971	0.82[AMR][1000 genomes]
rs3112183	0.92[EUR][1000 genomes]
rs3112184	0.82[AMR][1000 genomes]
rs3112186	0.82[AMR][1000 genomes]
rs3112188	0.82[AMR][1000 genomes]
rs3112189	0.82[AMR][1000 genomes]
rs3112191	0.82[AMR][1000 genomes]
rs3112192	0.82[AMR][1000 genomes]
rs3112196	0.85[AMR][1000 genomes]
rs3112198	0.83[AFR][1000 genomes]
rs3112200	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3112204	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3112205	1.00[ASN][1000 genomes]
rs3112209	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112210	0.93[ASN][1000 genomes]
rs3112215	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3112216	0.91[ASN][1000 genomes]
rs3134628	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3134629	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3134630	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35387882	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4602206	0.89[ASN][1000 genomes]
rs4630748	0.83[ASN][1000 genomes]
rs4670892	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4670894	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56393601	1.00[ASN][1000 genomes]
rs6544175	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6753251	0.97[ASN][1000 genomes]
rs7419616	0.85[ASN][1000 genomes]
rs7419838	0.91[ASN][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3099952	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:38994600-39004600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:38999400-39004600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:38999400-39004600	Weak transcription	A549	lung
5	chr2:39000000-39004800	Weak transcription	Fetal Intestine Small	intestine
6	chr2:39002600-39004600	Weak transcription	K562	blood
7	chr2:39003800-39004800	Enhancers	HepG2	liver
8	chr2:39004200-39004800	Flanking Active TSS	Placenta	Placenta
9	chr2:39004200-39005000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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