Variant report

Variant	rs2240823
Chromosome Location	chr7:38261921-38261922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:38147469..38148161-chr7:38261438..38262362,2	MCF-7	breast:
2	chr7:38145292..38146218-chr7:38261831..38262510,3	K562	blood:
3	chr7:38261793..38262727-chr7:38358272..38359096,4	MCF-7	breast:
4	chr7:38146737..38148304-chr7:38261624..38262803,9	K562	blood:
5	chr7:38261872..38262390-chr7:38358243..38358960,2	MCF-7	breast:
6	chr7:38255012..38257306-chr7:38260650..38262240,2	K562	blood:

Variant related genes	Relation type
ENSG00000211695	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1019179	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10255648	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10260257	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10260281	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10265931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10480165	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[ASN][1000 genomes]
rs11765477	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11773415	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12155081	0.81[YRI][hapmap]
rs12671662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171306	0.91[CHB][hapmap]
rs1860517	0.81[YRI][hapmap]
rs1860519	0.81[YRI][hapmap]
rs1860523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079850	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2191313	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4720272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4723736	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4723737	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59870865	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73128691	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9490	0.82[CHB][hapmap];0.81[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9801416	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016355	chr7:38168232-38372719	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv830963	chr7:38172988-38344779	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv830964	chr7:38218708-38390518	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1030349	chr7:38227528-38372719	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv538818	chr7:38227528-38372719	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv1025974	chr7:38227528-38503472	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv538819	chr7:38227528-38503472	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv433041	chr7:38229107-38358728	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv433044	chr7:38238119-38358728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	nsv1027803	chr7:38257707-38410660	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	nsv538820	chr7:38257707-38410660	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
16	nsv1020990	chr7:38257707-38503472	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
17	esv1799574	chr7:38259283-38265368	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv433047	chr7:38259354-38348812	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv433046	chr7:38259354-38351975	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
20	nsv433045	chr7:38259354-38358728	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
21	nsv870213	chr7:38261012-38382508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2240823	TARP	cis	parietal	SCAN
rs2240823	TBX20	cis	cerebellum	SCAN
rs2240823	STARD3NL	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38238600-38268800	Weak transcription	Esophagus	oesophagus
2	chr7:38251600-38270400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:38251800-38270200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:38252000-38272400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:38252000-38273000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:38253800-38267400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:38254400-38263200	Strong transcription	HSMMtube	muscle
8	chr7:38255000-38268800	Weak transcription	Gastric	stomach
9	chr7:38255400-38264800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:38255400-38267400	Weak transcription	Stomach Mucosa	stomach
11	chr7:38255400-38271800	Weak transcription	Small Intestine	intestine
12	chr7:38255600-38263000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:38255600-38264600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:38255600-38268600	Weak transcription	Pancreas	Pancrea
15	chr7:38255800-38262000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:38255800-38264400	Strong transcription	GM12878-XiMat	blood
17	chr7:38256000-38262000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr7:38256000-38263400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:38256000-38264400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr7:38256200-38262000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:38256200-38262000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr7:38256200-38262600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:38256200-38264400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:38256200-38264400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:38256200-38265400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr7:38256200-38268800	Strong transcription	HSMM	muscle
27	chr7:38256400-38262000	Strong transcription	Primary T cells from cord blood	blood
28	chr7:38256400-38263200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:38256400-38264400	Strong transcription	Fetal Lung	lung
30	chr7:38256400-38264400	Strong transcription	Fetal Stomach	stomach
31	chr7:38256400-38264600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:38256400-38264600	Strong transcription	HUVEC	blood vessel
33	chr7:38256600-38262400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr7:38256600-38263000	Strong transcription	Osteobl	bone
35	chr7:38256600-38266000	Weak transcription	Psoas Muscle	Psoas
36	chr7:38257000-38262000	Strong transcription	Fetal Intestine Large	intestine
37	chr7:38257000-38262000	Strong transcription	Dnd41	blood
38	chr7:38257200-38268600	Weak transcription	HepG2	liver
39	chr7:38257400-38262000	Strong transcription	Primary B cells from cord blood	blood
40	chr7:38257400-38262200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:38257400-38262200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr7:38257400-38264400	Strong transcription	Fetal Kidney	kidney
43	chr7:38257600-38262200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:38257600-38270800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:38257800-38270800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:38258000-38262000	Strong transcription	Fetal Thymus	thymus
47	chr7:38258000-38268800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr7:38258600-38262000	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr7:38259000-38263200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr7:38259200-38262000	Strong transcription	Brain Inferior Temporal Lobe	brain

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