Variant report

Variant	rs37976
Chromosome Location	chr7:8014957-8014958
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	chr7:8014833-8015188	GM12891	blood:	n/a	n/a
2	POLR2A	chr7:8013565-8015898	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:8014768-8015301	GM12892	blood:	n/a	n/a
4	POLR2A	chr7:8014603-8016004	GM12892	blood:	n/a	n/a
5	NFATC1	chr7:8014889-8015852	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:8014786-8015018	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr7:8014893-8015285	GM12891	blood:	n/a	n/a
8	POLR2A	chr7:8014673-8016665	GM12892	blood:	n/a	n/a
9	POLR2A	chr7:8014813-8015406	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:8014795-8016731	GM12892	blood:	n/a	n/a
11	RCOR1	chr7:8014736-8015116	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000233264	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10226865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10238003	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10253861	0.88[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs10264999	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10278726	1.00[CEU][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10278791	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10281919	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11981372	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1476823	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17568389	0.82[CEU][hapmap]
rs258850	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs258851	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs258852	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs37972	0.82[CHB][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs37973	0.82[CHB][hapmap];0.83[TSI][hapmap]
rs37974	0.83[MEX][hapmap]
rs37979	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs37982	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs37986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs37987	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs37996	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs37997	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs38000	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs38007	0.84[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs38008	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs38009	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs38015	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4256496	1.00[CEU][hapmap]
rs4725055	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4725056	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4725059	0.85[CEU][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6463753	0.96[CEU][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6953808	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7796831	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7808399	0.93[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7810540	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9655516	1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs37976	GLCCI1	cis	parietal	SCAN
rs37976	ZDHHC4	cis	parietal	SCAN
rs37976	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8010000-8016200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:8010000-8016200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:8010400-8015600	Weak transcription	Small Intestine	intestine
4	chr7:8010400-8016200	Weak transcription	Left Ventricle	heart
5	chr7:8010800-8023600	Weak transcription	Psoas Muscle	Psoas
6	chr7:8011000-8016800	Weak transcription	Osteobl	bone
7	chr7:8011400-8023600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:8012000-8015800	Weak transcription	Spleen	Spleen
9	chr7:8012000-8016200	Weak transcription	Fetal Stomach	stomach
10	chr7:8012000-8017400	Weak transcription	Placenta	Placenta
11	chr7:8012000-8017400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:8012000-8017400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr7:8012000-8017600	Weak transcription	Aorta	Aorta
14	chr7:8012000-8018600	Weak transcription	Adipose Nuclei	Adipose
15	chr7:8012000-8018800	Weak transcription	Fetal Lung	lung
16	chr7:8012000-8020000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:8012200-8015400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:8012200-8017000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:8012200-8017400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:8012200-8017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:8012200-8018000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr7:8012200-8018000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr7:8012200-8018400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:8012200-8020600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:8012400-8018200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr7:8012600-8016600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr7:8012800-8015600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr7:8012800-8015600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:8012800-8015600	Weak transcription	Fetal Thymus	thymus
30	chr7:8012800-8016200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:8012800-8017000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:8012800-8017200	Weak transcription	K562	blood
33	chr7:8012800-8017400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr7:8012800-8019200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr7:8012800-8019600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:8012800-8021000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:8013000-8015800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:8013000-8016400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr7:8013000-8017000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr7:8013000-8017600	Weak transcription	Liver	Liver
41	chr7:8013200-8015000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr7:8013200-8015200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr7:8013200-8015600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr7:8013200-8018000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr7:8013400-8016400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr7:8013400-8017000	Weak transcription	Fetal Heart	heart
47	chr7:8013400-8017400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:8013400-8017400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr7:8013400-8018000	Enhancers	Dnd41	blood
50	chr7:8013400-8029000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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