Variant report

Variant	rs37987
Chromosome Location	chr7:8024722-8024723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:8023684..8026582-chr7:8035460..8038247,2	MCF-7	breast:
2	chr7:8016682..8018691-chr7:8023208..8025599,2	MCF-7	breast:
3	chr7:8010105..8011990-chr7:8023943..8026240,3	MCF-7	breast:

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];0.86[CHB][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10238003	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10253861	0.88[CEU][hapmap]
rs10264999	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10278726	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10278791	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10281919	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11981372	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1476823	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17568389	0.83[CEU][hapmap]
rs258850	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs258851	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs258852	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs37972	0.80[YRI][hapmap]
rs37976	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]
rs37979	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37982	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs37986	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs37996	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs37997	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs38000	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs38007	0.85[CEU][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs38008	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs38009	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs38015	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4256496	1.00[CEU][hapmap]
rs4725055	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4725056	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4725059	0.85[CEU][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6463753	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6953808	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7796831	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7808399	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7810540	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9655516	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][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
rs37987	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8013400-8029000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr7:8013400-8029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:8014200-8028600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:8015000-8045000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:8015200-8031800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:8016600-8026800	Weak transcription	Thymus	Thymus
7	chr7:8016600-8027200	Weak transcription	Fetal Thymus	thymus
8	chr7:8017800-8029000	Weak transcription	Hela-S3	cervix
9	chr7:8017800-8029600	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:8017800-8029600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:8018000-8029000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:8019000-8031400	Weak transcription	Primary B cells from cord blood	blood
13	chr7:8019600-8029400	Weak transcription	Adipose Nuclei	Adipose
14	chr7:8020000-8024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:8020000-8027600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:8020400-8028200	Weak transcription	Fetal Heart	heart
17	chr7:8020600-8026800	Weak transcription	Dnd41	blood
18	chr7:8021600-8025200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr7:8021600-8029000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr7:8022000-8026600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr7:8022000-8028800	Weak transcription	Brain Germinal Matrix	brain
22	chr7:8023000-8025400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:8023000-8026000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr7:8023200-8025200	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr7:8023400-8025200	Enhancers	Liver	Liver
26	chr7:8023600-8024800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:8023600-8025600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr7:8023800-8028400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:8024000-8025000	Enhancers	Primary T cells from cord blood	blood
30	chr7:8024000-8025800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:8024000-8027200	Weak transcription	Psoas Muscle	Psoas
32	chr7:8024000-8028800	Weak transcription	Small Intestine	intestine
33	chr7:8024000-8029200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr7:8024200-8025000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:8024200-8025400	Weak transcription	GM12878-XiMat	blood
36	chr7:8024400-8024800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:8024400-8024800	Enhancers	Fetal Kidney	kidney
38	chr7:8024400-8025000	Enhancers	Osteobl	bone
39	chr7:8024600-8025600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr7:8024600-8026000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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