Variant report

Variant	rs38009
Chromosome Location	chr7:8042350-8042351
allele	C/G
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	chr7:8042031-8043634	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:8009265..8011101-chr7:8042338..8044850,2	MCF-7	breast:

Variant related genes	Relation type
GLCCI1	TF binding region
ENSG00000106415	Chromatin interaction
ENSG00000233108	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10226865	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10238003	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10253861	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs10264999	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs10278726	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10278791	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10281919	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11981372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1476823	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17568389	0.83[CEU][hapmap]
rs258850	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs258851	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs258852	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37976	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs37979	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs37982	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs37986	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs37987	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs37996	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs37997	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs38000	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38007	0.85[CEU][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs38008	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4256496	1.00[CEU][hapmap]
rs4725055	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4725056	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4725059	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6463753	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6463758	0.81[AMR][1000 genomes]
rs6953808	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7796831	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7808399	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7810540	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9655516	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs38009	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8015000-8045000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:8029200-8043600	Weak transcription	Small Intestine	intestine
3	chr7:8029800-8046400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:8029800-8049000	Weak transcription	Fetal Heart	heart
5	chr7:8033600-8043600	Weak transcription	Primary B cells from cord blood	blood
6	chr7:8035200-8045000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:8036000-8044200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:8036400-8043600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:8036400-8044400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:8036400-8044400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:8036400-8045000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:8036400-8046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:8036400-8077400	Weak transcription	Right Ventricle	heart
14	chr7:8036600-8044200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr7:8036600-8044600	Weak transcription	Osteobl	bone
16	chr7:8036600-8045600	Weak transcription	Liver	Liver
17	chr7:8036600-8045600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr7:8036600-8045800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:8036600-8045800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:8036600-8053800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr7:8036600-8057200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr7:8036600-8064400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:8036600-8064400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:8036600-8074600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:8036800-8042800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:8036800-8043200	Weak transcription	Hela-S3	cervix
27	chr7:8036800-8043800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr7:8036800-8043800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:8036800-8044200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:8036800-8046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:8037400-8043800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr7:8037400-8044200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:8038000-8066000	Weak transcription	Pancreas	Pancrea
34	chr7:8038200-8043600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr7:8038200-8045800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:8038400-8046400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:8038400-8066000	Weak transcription	Spleen	Spleen
38	chr7:8039200-8044400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:8039400-8044200	Weak transcription	Thymus	Thymus
40	chr7:8039400-8045200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr7:8039400-8046400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:8039400-8046400	Weak transcription	Left Ventricle	heart
43	chr7:8039400-8046400	Weak transcription	Ovary	ovary
44	chr7:8039600-8043000	Weak transcription	Fetal Thymus	thymus
45	chr7:8039600-8043200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr7:8039800-8042800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr7:8040000-8046400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:8040400-8043000	Weak transcription	Dnd41	blood
49	chr7:8040600-8044200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr7:8041000-8044200	Weak transcription	Rectal Mucosa Donor 29	rectum

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