Variant report

Variant	rs7626871
Chromosome Location	chr3:141160882-141160883
allele	A/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	PAX5	chr3:141160544-141160902	GM12878	blood:	n/a	chr3:141160604-141160623
2	POLR2A	chr3:141159946-141163964	U87	brain:	n/a	n/a
3	PAX5	chr3:141160234-141160909	GM12878	blood:	n/a	chr3:141160604-141160623
4	CTCF	chr3:141160780-141160930	HPF	lung:	n/a	n/a
5	POLR2A	chr3:141160078-141161323	GM12878	blood:	n/a	n/a
6	RUNX3	chr3:141160043-141160885	GM12878	blood:	n/a	n/a
7	IKZF1	chr3:141160152-141160931	GM12878	blood:	n/a	n/a
8	MTA3	chr3:141159927-141160924	GM12878	blood:	n/a	n/a
9	CTCF	chr3:141160820-141160970	HVMF	connective:	n/a	n/a
10	JUND	chr3:141160076-141161170	GM12878	blood:	n/a	chr3:141160362-141160374 chr3:141160247-141160261 chr3:141160363-141160372 chr3:141160363-141160373 chr3:141160364-141160373 chr3:141160362-141160373
11	STAT5A	chr3:141159949-141161027	GM12878	blood:	n/a	chr3:141160932-141160944 chr3:141160824-141160832 chr3:141160364-141160373
12	PAX5	chr3:141160105-141160894	GM12878	blood:	n/a	chr3:141160604-141160623

No.	Distal block	Cell Line	Cell type
1	chr3:141158978..141161991-chr3:141166297..141169047,4	K562	blood:
2	chr3:141159186..141161799-chr3:141162940..141165870,2	MCF-7	breast:
3	chr3:141022322..141022899-chr3:141160380..141160883,2	K562	blood:
4	chr3:141079580..141080372-chr3:141159972..141160950,4	MCF-7	breast:
5	chr3:141159442..141161991-chr3:141166297..141167819,2	K562	blood:
6	chr3:141153683..141156573-chr3:141158682..141161645,2	K562	blood:
7	chr3:141157834..141161364-chr3:141205126..141207553,3	K562	blood:
8	chr3:141158936..141162571-chr3:141173016..141176156,4	MCF-7	breast:
9	chr3:141160372..141162712-chr3:141168318..141171011,2	MCF-7	breast:
10	chr3:141160175..141161761-chr3:141162078..141164256,2	MCF-7	breast:
11	chr3:141157834..141161921-chr3:141205126..141207972,3	K562	blood:
12	chr3:141028495..141032567-chr3:141157435..141162053,7	K562	blood:
13	chr3:141087251..141089777-chr3:141160023..141161997,3	K562	blood:

Variant related genes	Relation type
ZBTB38	TF binding region
ENSG00000177311	Chromatin interaction
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs16851435	0.91[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16851438	0.82[CEU][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16851441	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16851483	0.88[JPT][hapmap]
rs2035935	0.88[JPT][hapmap]
rs2035936	0.82[JPT][hapmap]
rs2312193	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2639997	0.88[JPT][hapmap]
rs2640017	0.88[JPT][hapmap]
rs295299	0.88[JPT][hapmap]
rs295300	0.88[JPT][hapmap]
rs3732869	0.89[JPT][hapmap]
rs3821709	0.88[JPT][hapmap]
rs4683404	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683610	0.88[JPT][hapmap]
rs62282002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627807	0.88[JPT][hapmap]
rs9878347	0.83[JPT][hapmap]
rs9879503	0.83[JPT][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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7626871	ZBTB38	cis	multi-tissue	Pritchard
rs7626871	FLJ35036	cis	multi-tissue	Pritchard
rs7626871	ENSG00000177311	cis	multi-tissue	Pritchard
rs7626871	ZBTB38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141131800-141161200	Weak transcription	Thymus	Thymus
2	chr3:141132200-141171000	Weak transcription	Primary B cells from cord blood	blood
3	chr3:141134000-141161600	Weak transcription	Fetal Brain Male	brain
4	chr3:141134200-141161600	Weak transcription	Primary T cells from cord blood	blood
5	chr3:141145400-141161200	Weak transcription	Fetal Brain Female	brain
6	chr3:141145400-141161800	Weak transcription	Esophagus	oesophagus
7	chr3:141145800-141161600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:141147000-141161200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:141147000-141161200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:141148800-141161600	Weak transcription	Brain Germinal Matrix	brain
11	chr3:141148800-141161600	Weak transcription	Spleen	Spleen
12	chr3:141148800-141161800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:141148800-141164200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:141149400-141164200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:141149600-141161200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:141150800-141161200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:141153200-141161600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:141153200-141164000	Weak transcription	Psoas Muscle	Psoas
19	chr3:141155000-141161400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:141155400-141161200	Weak transcription	Liver	Liver
21	chr3:141155400-141170800	Weak transcription	Fetal Thymus	thymus
22	chr3:141156200-141161800	Weak transcription	Ovary	ovary
23	chr3:141156400-141161600	Weak transcription	Colonic Mucosa	Colon
24	chr3:141156400-141161800	Weak transcription	Gastric	stomach
25	chr3:141156400-141161800	Weak transcription	Pancreas	Pancrea
26	chr3:141156400-141166600	Strong transcription	Fetal Intestine Large	intestine
27	chr3:141157600-141161600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:141157800-141161200	Weak transcription	Aorta	Aorta
29	chr3:141157800-141161200	Enhancers	Colon Smooth Muscle	Colon
30	chr3:141157800-141161200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:141157800-141161400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:141157800-141161800	Weak transcription	Lung	lung
33	chr3:141158200-141161000	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:141158200-141161200	Weak transcription	Adipose Nuclei	Adipose
35	chr3:141158400-141161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:141158600-141161200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:141158600-141161200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:141158600-141161200	Enhancers	Rectal Smooth Muscle	rectum
39	chr3:141158600-141161400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:141159000-141161000	Weak transcription	Fetal Kidney	kidney
41	chr3:141159000-141161400	Weak transcription	HSMMtube	muscle
42	chr3:141159200-141161000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:141159200-141161200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:141159200-141161200	Enhancers	Osteobl	bone
45	chr3:141159400-141161000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:141159400-141161200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:141159400-141161400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:141159400-141161400	Weak transcription	Brain Angular Gyrus	brain
49	chr3:141159400-141161600	Enhancers	Fetal Heart	heart
50	chr3:141159400-141162200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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