Variant report

Variant	rs2197205
Chromosome Location	chr3:111758076-111758077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr3:111757710-111758080	GM12891	blood:	n/a	chr3:111757839-111757848
2	POLR2A	chr3:111757689-111758204	H1-neurons	neurons:	n/a	n/a
3	SPI1	chr3:111757491-111758178	GM12878	blood:	n/a	chr3:111757839-111757848
4	GATA3	chr3:111757689-111758128	T-47D	breast:	n/a	n/a
5	REST	chr3:111757689-111758236	H1-neurons	neurons:	n/a	n/a
6	TEAD4	chr3:111757615-111758165	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr3:111757692-111758253	H1-neurons	neurons:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:111758050-111758100	ECC-1	luminal epithelium:	n/a
2	chr3:111758050-111758100	MCF10A-Er-Src	breast:	n/a
3	chr3:111758050-111758100	NT2-D1	testis:	n/a
4	chr3:111758050-111758100	HRPEpiC	eye:	n/a
5	chr3:111758050-111758100	IMR90	lung:	fetal
6	chr3:111758050-111758100	GM06990	blood:	n/a
7	chr3:111758050-111758100	PANC-1	pancreas:	n/a
8	chr3:111758050-111758100	CMK	blood:	n/a
9	chr3:111758050-111758100	HepG2	liver:	n/a
10	chr3:111758050-111758100	U87	brain:	n/a
11	chr3:111758050-111758100	GM12891	blood:	n/a
12	chr3:111758050-111758100	HRE	kidney:	n/a
13	chr3:111758050-111758100	BJ	skin:	n/a
14	chr3:111758050-111758100	HL-60	blood:	n/a
15	chr3:111758050-111758100	A549	lung:	n/a
16	chr3:111758050-111758100	AG09309	skin:	n/a
17	chr3:111758050-111758100	SAEC	small airway:	n/a
18	chr3:111758050-111758100	SK-N-SH_RA	brain:	n/a
19	chr3:111758050-111758100	K562	blood:	n/a
20	chr3:111758050-111758100	HCT-116	colon:	n/a
21	chr3:111758050-111758100	PFSK-1	brain:	n/a
22	chr3:111758050-111758100	HMEC	breast:	n/a
23	chr3:111758050-111758100	SKMC	muscle:	n/a
24	chr3:111758050-111758100	SK-N-MC	brain:	n/a
25	chr3:111758050-111758100	HEK293	kidney:	embryo
26	chr3:111758050-111758100	SK-N-SH	brain:	n/a
27	chr3:111758050-111758100	HAEpiC	amniotic membrane:	n/a
28	chr3:111758050-111758100	GM12878	blood:	n/a
29	chr3:111758050-111758100	HCPEpiC	choroid plexus:	n/a
30	chr3:111758050-111758100	AoSMC	blood vessel:	n/a
31	chr3:111758050-111758100	AG04449	skin:	fetal
32	chr3:111758050-111758100	AG10803	skin:	n/a
33	chr3:111758050-111758100	ovcar-3	ovarian:	n/a
34	chr3:111758050-111758100	ProgFib	skin:	n/a
35	chr3:111758050-111758100	Jurkat	blood:	n/a
36	chr3:111758050-111758100	GM19239	blood:	n/a
37	chr3:111758050-111758100	MCF-7	breast:	n/a
38	chr3:111758050-111758100	AG04450	lung:	fetal
39	chr3:111758050-111758100	HEEpiC	esophagus:	n/a
40	chr3:111758050-111758100	BE2_C	brain:	n/a
41	chr3:111758050-111758100	PrEC	prostate:	n/a
42	chr3:111758050-111758100	AG09319	gingival:	n/a
43	chr3:111758050-111758100	HNPCEpiC	eye:	n/a
44	chr3:111758050-111758100	GM12892	blood:	n/a
45	chr3:111758050-111758100	LNCaP	prostate:	n/a
46	chr3:111758050-111758100	Hepatocyte	liver:	n/a
47	chr3:111758050-111758100	HUVEC	blood vessel:	n/a
48	chr3:111758050-111758100	NH-A	brain:	n/a
49	chr3:111758050-111758100	HIPEpiC	eye:	n/a
50	chr3:111758050-111758100	NHDF-neo	bronchial:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111757946..111760451-chr3:111761059..111762628,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMPRSS7	TF binding region
TMPRSS7	CpG island
ENSG00000176040	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1001516	0.91[EUR][1000 genomes]
rs10934129	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12485636	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12490294	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12492101	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12492109	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12492150	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12495270	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12495510	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12495567	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12496749	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13434231	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530343	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1574737	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1907642	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1907643	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2197206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2218325	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2218326	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2399402	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34328343	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34353553	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4343597	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4386465	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4588336	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4682069	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4682070	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4682072	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4682073	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682074	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682078	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682330	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4682331	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4682332	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4682333	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4682334	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4682335	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4682336	0.91[EUR][1000 genomes]
rs4682337	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4682338	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4682339	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4682342	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682343	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682344	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682345	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682346	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682347	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682348	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56164807	0.80[EUR][1000 genomes]
rs6771549	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6777972	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6781582	0.91[EUR][1000 genomes]
rs6783542	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6785244	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6795242	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs729801	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73216064	0.81[EUR][1000 genomes]
rs73216065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73216066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7621126	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7651134	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7651142	0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs976758	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs976759	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs981267	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9817034	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9823102	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9831037	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9831043	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9833495	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9834130	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9836405	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9838617	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9838732	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9838788	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9839073	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9840207	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9843120	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9848208	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9856396	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9858952	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9862289	0.81[EUR][1000 genomes]
rs9862414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9864148	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9864788	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9868274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9868331	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9868654	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9868673	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9871103	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9871444	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9873914	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9874652	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9874944	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9876283	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9876569	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2197205	TMPRSS7	cis	cerebellum	SCAN
rs2197205	TAGLN3	cis	cerebellum	SCAN
rs2197205	TMPRSS7	cis	parietal	SCAN
rs2197205	CD96	cis	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111754400-111762600	Weak transcription	Fetal Heart	heart
2	chr3:111754600-111758200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:111756200-111763200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:111756800-111759200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:111757400-111758200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:111757400-111758200	Enhancers	HSMM	muscle
7	chr3:111757400-111758400	Enhancers	Primary B cells from peripheral blood	blood
8	chr3:111757400-111758400	Enhancers	NHEK	skin
9	chr3:111757400-111758600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:111757400-111758600	Enhancers	HSMMtube	muscle
11	chr3:111757600-111758800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:111757600-111767800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:111757800-111758200	Enhancers	A549	lung
14	chr3:111757800-111758600	Enhancers	GM12878-XiMat	blood
15	chr3:111758000-111758200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:111758000-111758400	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr3:111758000-111762400	Weak transcription	HMEC	breast

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