Variant report

Variant	rs7571942
Chromosome Location	chr2:112913501-112913502
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	ELF1	chr2:112913024-112913603	GM12878	blood:	n/a	n/a
2	PAX5	chr2:112913458-112913847	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:112911308..112914054-chr2:113031885..113034558,2	K562	blood:
2	chr2:112894459..112897038-chr2:112912289..112914115,2	MCF-7	breast:
3	chr2:112911116..112914054-chr2:113031578..113034558,3	K562	blood:
4	chr2:112912607..112915274-chr2:112919768..112922184,2	K562	blood:

Variant related genes	Relation type
FBLN7	TF binding region
ENSG00000144152	Chromatin interaction
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10189625	0.85[JPT][hapmap]
rs10196498	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10207420	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11123128	0.92[JPT][hapmap]
rs11675443	0.92[JPT][hapmap]
rs1316488	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1320360	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2312697	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4318395	0.84[JPT][hapmap]
rs4411701	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4848272	0.92[JPT][hapmap]
rs4849045	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4849046	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4849048	0.85[JPT][hapmap];0.80[TSI][hapmap]
rs6542041	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6755850	1.00[CEU][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7575979	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7593053	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7607362	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv874866	chr2:112906599-112991098	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7571942	FBLN7	cis	cerebellum	SCAN
rs7571942	PSD4	cis	parietal	SCAN
rs7571942	POLR1B	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112896400-112934600	Weak transcription	Aorta	Aorta
2	chr2:112898200-112915000	Weak transcription	Pancreas	Pancrea
3	chr2:112899200-112914000	Weak transcription	HepG2	liver
4	chr2:112900200-112913600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:112900600-112931400	Weak transcription	Fetal Lung	lung
6	chr2:112907200-112920400	Weak transcription	Right Atrium	heart
7	chr2:112907400-112914200	Enhancers	HSMM	muscle
8	chr2:112907600-112914400	Enhancers	HSMMtube	muscle
9	chr2:112908400-112914000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:112908800-112913800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:112908800-112914000	Weak transcription	HMEC	breast
12	chr2:112909200-112914000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:112911200-112914000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:112911400-112913800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:112911600-112913600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:112911600-112914000	Weak transcription	NHDF-Ad	bronchial
17	chr2:112911800-112914800	Enhancers	Fetal Thymus	thymus
18	chr2:112912000-112913600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:112912000-112915200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:112912200-112914400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:112912200-112914600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr2:112912200-112914600	Enhancers	Fetal Muscle Leg	muscle
23	chr2:112912400-112915000	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:112912600-112913600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:112912600-112914400	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:112912600-112927200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:112912800-112913800	Enhancers	Primary B cells from cord blood	blood
28	chr2:112912800-112913800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr2:112912800-112913800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:112912800-112913800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
31	chr2:112912800-112914000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:112912800-112914400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr2:112912800-112914400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr2:112912800-112914400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr2:112912800-112914600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:112912800-112914600	Enhancers	Spleen	Spleen
37	chr2:112913000-112913600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:112913000-112913600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
39	chr2:112913000-112913800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:112913000-112913800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr2:112913000-112913800	Enhancers	Colonic Mucosa	Colon
42	chr2:112913000-112913800	Flanking Active TSS	Thymus	Thymus
43	chr2:112913000-112913800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr2:112913000-112914200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:112913000-112914200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr2:112913000-112914200	Enhancers	HUVEC	blood vessel
47	chr2:112913000-112914400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr2:112913000-112914400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:112913000-112914600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr2:112913000-112914600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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