Variant report

Variant	rs7971
Chromosome Location	chr7:21940960-21940961
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:21938917..21941313-chr7:21945922..21947681,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1128226	0.92[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs11761264	0.91[CHD][hapmap]
rs11763022	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs11763025	0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs11763709	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs11769521	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12540021	0.90[ASW][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs17361667	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs4487645	0.86[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4636103	0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap]
rs55714084	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56249828	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56333627	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57104699	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6948632	0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs7785157	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1027453	chr7:21918474-21982448	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7971	TWIST1	cis	cerebellum	SCAN
rs7971	CXCL13	trans	parietal	SCAN
rs7971	MACC1	cis	parietal	SCAN
rs7971	CDCA7L	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21924400-21945400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:21926600-21942600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:21928000-21942600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:21931000-21942400	Weak transcription	Fetal Kidney	kidney
5	chr7:21932600-21942000	Weak transcription	Brain Germinal Matrix	brain
6	chr7:21932600-21951000	Weak transcription	HSMM	muscle
7	chr7:21933000-21963200	Weak transcription	A549	lung
8	chr7:21934000-21950400	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:21934200-21951600	Weak transcription	Fetal Brain Male	brain
10	chr7:21935200-21942200	Weak transcription	HMEC	breast
11	chr7:21936400-21942400	Weak transcription	NH-A	brain
12	chr7:21936600-21942000	Weak transcription	HSMMtube	muscle
13	chr7:21936600-21956400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr7:21936600-21956600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:21936800-21945200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:21936800-21945200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:21937000-21942200	Weak transcription	Brain Angular Gyrus	brain
18	chr7:21937000-21952200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:21937000-21956400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:21937200-21956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:21937400-21950800	Weak transcription	Right Atrium	heart
22	chr7:21937400-21956000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:21937600-21941800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:21937600-21942400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr7:21937600-21952000	Weak transcription	Psoas Muscle	Psoas
26	chr7:21937600-21952800	Strong transcription	Thymus	Thymus
27	chr7:21937600-21956200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:21937600-21956400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr7:21937800-21947800	Strong transcription	NHEK	skin
30	chr7:21937800-21950200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr7:21937800-21950600	Strong transcription	Fetal Stomach	stomach
32	chr7:21937800-21954000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:21937800-21956000	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr7:21937800-21956200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr7:21938000-21941000	Strong transcription	Pancreas	Pancrea
36	chr7:21938000-21941400	Strong transcription	Fetal Lung	lung
37	chr7:21938000-21942000	Strong transcription	HUVEC	blood vessel
38	chr7:21938000-21942200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:21938000-21942200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr7:21938000-21942400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:21938000-21949600	Strong transcription	Fetal Muscle Leg	muscle
42	chr7:21938000-21955000	Weak transcription	Stomach Mucosa	stomach
43	chr7:21938000-21956200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr7:21938200-21942000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:21938200-21942000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:21938200-21949200	Strong transcription	Hela-S3	cervix
47	chr7:21938200-21950000	Weak transcription	Small Intestine	intestine
48	chr7:21938400-21941200	Strong transcription	Brain Anterior Caudate	brain
49	chr7:21938400-21945400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr7:21938400-21948600	Strong transcription	Rectal Smooth Muscle	rectum

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