Variant report

Variant	rs708611
Chromosome Location	chr1:155743310-155743311
allele	G/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	TCF7L2	chr1:155743078-155743518	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
GON4L	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10908479	0.85[CHB][hapmap]
rs10908481	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs10908482	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11264409	0.92[ASN][1000 genomes]
rs11264410	0.96[ASN][1000 genomes]
rs11264413	0.83[ASN][1000 genomes]
rs12024257	0.80[ASN][1000 genomes]
rs12035524	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs12040894	0.93[ASN][1000 genomes]
rs12047756	0.85[CHB][hapmap]
rs12081192	0.89[ASN][1000 genomes]
rs12407800	0.87[ASN][1000 genomes]
rs12744132	0.90[CHB][hapmap]
rs2048431	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs2175391	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs2297775	0.99[ASN][1000 genomes]
rs28582361	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28662267	0.85[ASN][1000 genomes]
rs2948071	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2948072	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2985707	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs348196	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs3738590	0.84[CHB][hapmap];0.97[CHD][hapmap]
rs3820594	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs4278368	0.93[ASN][1000 genomes]
rs475550	0.97[CHD][hapmap]
rs490608	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6427286	0.95[CHB][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427287	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs644853	0.87[YRI][hapmap]
rs6657670	0.83[ASN][1000 genomes]
rs6662953	0.91[ASN][1000 genomes]
rs6665227	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs670876	0.85[CHB][hapmap]
rs729022	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs7541060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7550402	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs821551	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs822025	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs822478	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs822490	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs822505	0.82[CEU][hapmap]
rs822508	0.82[CEU][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap]
rs822527	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs860295	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9426933	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv872469	chr1:155743310-155810293	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs708611	RIT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155715400-155789200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:155715600-155764600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:155716000-155793400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:155716600-155781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:155717200-155761000	Strong transcription	Fetal Stomach	stomach
6	chr1:155717400-155795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:155717600-155750200	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:155720200-155745400	Strong transcription	Fetal Muscle Leg	muscle
9	chr1:155720200-155748600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:155720200-155748800	Strong transcription	Duodenum Mucosa	Duodenum
11	chr1:155720200-155748800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr1:155720200-155749000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:155720200-155749600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:155720200-155750200	Strong transcription	Primary T cells from cord blood	blood
15	chr1:155720200-155750600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:155720200-155755800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:155720200-155756200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:155720200-155756600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:155720200-155798200	Strong transcription	Fetal Thymus	thymus
20	chr1:155720200-155803600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:155720400-155750200	Strong transcription	Adipose Nuclei	Adipose
22	chr1:155720400-155750400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:155720400-155750600	Strong transcription	Dnd41	blood
24	chr1:155720400-155755600	Strong transcription	Placenta	Placenta
25	chr1:155720400-155756400	Strong transcription	Liver	Liver
26	chr1:155720400-155760800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:155720400-155796800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:155720600-155743600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:155720600-155757200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:155720800-155747600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:155720800-155749000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:155721000-155748800	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:155725000-155748600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:155726000-155747400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:155727200-155754200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:155728600-155747600	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr1:155729400-155747600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:155730400-155764200	Weak transcription	Psoas Muscle	Psoas
39	chr1:155730800-155748000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:155731000-155748800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:155732200-155789200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:155732400-155755600	Strong transcription	Fetal Intestine Large	intestine
43	chr1:155732600-155748800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:155733800-155743400	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:155734000-155748800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:155734400-155746200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:155734400-155747800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:155734600-155743800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:155734600-155748000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:155734600-155748000	Strong transcription	Osteobl	bone

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