Variant report

Variant	rs38474
Chromosome Location	chr7:30595869-30595870
allele	A/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	SPI1	chr7:30595811-30596191	GM12891	blood:	n/a	chr7:30595999-30596008
2	BHLHE40	chr7:30595868-30596082	GM12878	blood:	n/a	n/a
3	SPI1	chr7:30595853-30596169	GM12878	blood:	n/a	chr7:30595999-30596008
4	SPI1	chr7:30595816-30596110	GM12891	blood:	n/a	chr7:30595999-30596008

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:30595663..30599818-chr7:30601327..30605437,5	K562	blood:
2	chr7:30595359..30598170-chr7:30599924..30602926,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCT-1	chr7:30587973-30601744	ENSG00000196295.7

Variant related genes	Relation type
GGCT	TF binding region
ENSG00000196295	TF binding region
ENSG00000196295	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs2709787	0.84[EUR][1000 genomes]
rs2709790	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28679	0.89[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38409	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap]
rs38410	0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38411	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38413	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38414	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38415	0.91[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs38416	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38417	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38418	0.81[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38419	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38420	0.93[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38422	0.84[ASN][1000 genomes]
rs38423	0.83[ASN][1000 genomes]
rs38425	0.83[ASN][1000 genomes]
rs38426	0.83[ASN][1000 genomes]
rs38427	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38429	0.83[ASN][1000 genomes]
rs38430	0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs38432	0.83[ASN][1000 genomes]
rs38433	0.91[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs38434	0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs38435	0.84[EUR][1000 genomes]
rs38436	0.84[EUR][1000 genomes]
rs38437	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38438	0.84[ASN][1000 genomes]
rs38440	0.87[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38441	0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs38442	0.89[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs38443	0.80[ASN][1000 genomes]
rs38444	0.90[ASN][1000 genomes]
rs38445	0.92[ASN][1000 genomes]
rs38446	0.92[ASN][1000 genomes]
rs38447	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38448	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38450	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38451	0.90[ASN][1000 genomes]
rs38452	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38453	0.93[ASN][1000 genomes]
rs38454	0.93[ASN][1000 genomes]
rs38455	0.90[ASN][1000 genomes]
rs38456	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38458	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38459	0.93[EUR][1000 genomes]
rs38460	0.93[ASN][1000 genomes]
rs38461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38462	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38463	0.93[ASN][1000 genomes]
rs38464	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38465	0.92[ASN][1000 genomes]
rs38466	0.91[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs38467	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs38468	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs38469	0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs38471	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38472	0.97[ASN][1000 genomes]
rs38473	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38478	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38480	0.95[ASN][1000 genomes]
rs38481	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38482	0.92[ASN][1000 genomes]
rs38483	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38485	0.86[EUR][1000 genomes]
rs38487	0.82[CHD][hapmap]
rs38488	0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs38498	0.81[EUR][1000 genomes]
rs39738	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs40237	0.83[ASN][1000 genomes]
rs4258	0.90[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs4259	0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4260	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs973002	0.86[CHB][hapmap];0.89[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs38474	AC005154.6	cis	Stomach	GTEx
rs38474	AC005154.8	cis	Whole Blood	GTEx
rs38474	AC005154.6	cis	Thyroid	GTEx
rs38474	AC005154.6	cis	lung	GTEx
rs38474	AC005154.6	cis	Esophagus Mucosa	GTEx
rs38474	AC005154.8	cis	Thyroid	GTEx
rs38474	AC005154.6	cis	Artery Tibial	GTEx
rs38474	AC005154.6	cis	Muscle Skeletal	GTEx
rs38474	AC005154.6	cis	Artery Aorta	GTEx
rs38474	AC005154.8	cis	lung	GTEx
rs38474	LOC401320	cis	uninvolved skin	skin_eQTL
rs38474	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38474	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38474	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38474	AC005154.6	cis	Nerve Tibial	GTEx
rs38474	AC005154.8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30554400-30596400	Weak transcription	Fetal Brain Female	brain
2	chr7:30561600-30606400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:30563000-30599800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:30564400-30612200	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:30569000-30602600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:30574800-30601000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:30575600-30600000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr7:30578000-30598200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr7:30578200-30601200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:30586200-30601400	Weak transcription	Gastric	stomach
11	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus
12	chr7:30586800-30596200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:30587200-30602400	Weak transcription	Ovary	ovary
14	chr7:30587600-30596000	Weak transcription	Aorta	Aorta
15	chr7:30589200-30596200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:30589600-30598800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:30590000-30600400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:30590200-30602600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr7:30590800-30597800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:30591000-30596000	Weak transcription	Brain Angular Gyrus	brain
21	chr7:30591000-30596000	Weak transcription	Fetal Brain Male	brain
22	chr7:30591000-30596200	Weak transcription	Fetal Intestine Small	intestine
23	chr7:30591000-30596200	Weak transcription	Lung	lung
24	chr7:30591000-30596200	Weak transcription	Spleen	Spleen
25	chr7:30591000-30599000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:30591000-30601400	Weak transcription	Colonic Mucosa	Colon
27	chr7:30591200-30596000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:30591200-30596000	Weak transcription	Brain Anterior Caudate	brain
29	chr7:30591200-30596200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:30591200-30596200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:30591200-30596200	Weak transcription	Brain Substantia Nigra	brain
32	chr7:30591200-30596200	Weak transcription	Esophagus	oesophagus
33	chr7:30591200-30596600	Weak transcription	Brain Hippocampus Middle	brain
34	chr7:30591200-30598000	Weak transcription	HSMMtube	muscle
35	chr7:30591200-30598200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr7:30591200-30598400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr7:30591200-30599000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr7:30591200-30599800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr7:30591200-30600200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:30591200-30600200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr7:30591200-30600200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:30591200-30600200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr7:30591200-30600200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr7:30591200-30600400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:30591200-30600400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:30591200-30601000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr7:30591200-30601000	Weak transcription	Pancreas	Pancrea
48	chr7:30591200-30602000	Weak transcription	Right Atrium	heart
49	chr7:30591200-30602600	Weak transcription	Right Ventricle	heart
50	chr7:30591200-30602600	Weak transcription	Thymus	Thymus

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