Variant report

Variant	rs12673417
Chromosome Location	chr7:120480687-120480688
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	POLR2A	chr7:120480558-120480933	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120474789..120476459-chr7:120479485..120482303,2	K562	blood:

Variant related genes	Relation type
TSPAN12	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10274689	0.81[CEU][hapmap]
rs114420	0.93[ASN][1000 genomes]
rs11976580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12154976	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17132731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17142976	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17143013	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2189974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2525706	0.81[ASN][1000 genomes]
rs2525710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs2721329	0.81[ASN][1000 genomes]
rs2721330	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs2721332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721344	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721348	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721360	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2721371	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs41613	1.00[ASN][1000 genomes]
rs41616	1.00[ASN][1000 genomes]
rs41617	1.00[ASN][1000 genomes]
rs41622	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41623	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41626	1.00[ASN][1000 genomes]
rs42333	1.00[ASN][1000 genomes]
rs4730982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55733320	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55749650	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56023697	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56067931	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61481874	0.93[ASN][1000 genomes]
rs67679138	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953454	0.81[CEU][hapmap]
rs73427871	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73427873	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73427878	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73721472	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7805733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7810542	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996903	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv5929	chr7:120467591-120513472	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120443000-120488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:120445200-120494400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:120466800-120482400	Weak transcription	Small Intestine	intestine
4	chr7:120468600-120482200	Weak transcription	Pancreas	Pancrea
5	chr7:120468600-120482400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr7:120468600-120483200	Weak transcription	Right Ventricle	heart
7	chr7:120468600-120487600	Weak transcription	Lung	lung
8	chr7:120470600-120484600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:120473800-120482000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:120474000-120482000	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:120474000-120482200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:120474000-120482200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:120474000-120492400	Weak transcription	Fetal Lung	lung
14	chr7:120474000-120496400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:120474400-120481200	Strong transcription	Fetal Intestine Large	intestine
16	chr7:120474600-120496600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr7:120476400-120484200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:120476600-120482200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:120476600-120492400	Weak transcription	Gastric	stomach
20	chr7:120477000-120481200	Weak transcription	Liver	Liver
21	chr7:120477000-120482200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:120477000-120482400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr7:120477000-120489800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr7:120477000-120492400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr7:120477200-120496200	Weak transcription	Aorta	Aorta
26	chr7:120478000-120481800	Weak transcription	Fetal Intestine Small	intestine
27	chr7:120478000-120482200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:120478000-120483400	Weak transcription	Fetal Stomach	stomach
29	chr7:120478000-120483400	Weak transcription	Left Ventricle	heart
30	chr7:120478200-120482200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:120478200-120482200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr7:120478400-120487400	Weak transcription	Colonic Mucosa	Colon
33	chr7:120478800-120482400	Weak transcription	Fetal Muscle Leg	muscle
34	chr7:120478800-120483200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr7:120479000-120482000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:120479200-120482000	Weak transcription	Fetal Kidney	kidney
37	chr7:120479200-120482200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr7:120479400-120484000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:120479400-120488000	Weak transcription	Right Atrium	heart
40	chr7:120479600-120481000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr7:120479600-120481200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr7:120479600-120481800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:120479600-120494000	Weak transcription	HUVEC	blood vessel
44	chr7:120479800-120481200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:120479800-120481400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr7:120479800-120481800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr7:120480000-120482200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:120480000-120482600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:120480000-120488000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:120480200-120481400	Enhancers	Pancreatic Islets	Pancreatic Islet

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