Variant report

Variant	rs12671604
Chromosome Location	chr7:129108517-129108518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:129099938..129101762-chr7:129105861..129110289,3	K562	blood:
2	chr7:129102197..129105819-chr7:129107947..129111490,3	K562	blood:
3	chr7:129075846..129077779-chr7:129107169..129109635,2	MCF-7	breast:
4	chr7:129106613..129108809-chr7:129119853..129122619,2	K562	blood:
5	chr7:129099938..129101762-chr7:129105861..129111774,4	K562	blood:
6	chr7:129106941..129109739-chr7:129249383..129251712,2	K562	blood:

Variant related genes	Relation type
ENSG00000273329	Chromatin interaction
ENSG00000106459	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1000676	0.84[TSI][hapmap]
rs10500117	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10954230	0.86[TSI][hapmap]
rs10954233	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10954234	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12155142	0.87[EUR][1000 genomes]
rs12540568	0.80[CHD][hapmap];0.84[TSI][hapmap]
rs12667132	0.82[TSI][hapmap]
rs12667232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34000750	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34794308	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34916100	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35131522	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35277123	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35544616	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4728163	0.80[CHD][hapmap];0.91[TSI][hapmap]
rs4728164	0.86[TSI][hapmap]
rs4728165	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4731578	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4731579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731580	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4731581	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4731582	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4731583	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs598412	0.91[CHD][hapmap]
rs62489110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs644723	0.85[JPT][hapmap]
rs691124	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs691158	0.86[JPT][hapmap]
rs691435	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs691555	0.86[CHD][hapmap]
rs692697	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs6943021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966481	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv831128	chr7:129063040-129240800	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12671604	AHCYL2	cis	parietal	SCAN
rs12671604	IRF5	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129076000-129110000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:129077400-129109400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:129080000-129128000	Weak transcription	HUVEC	blood vessel
4	chr7:129083800-129112800	Strong transcription	K562	blood
5	chr7:129089400-129110000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:129089600-129110200	Weak transcription	Brain Substantia Nigra	brain
7	chr7:129091600-129109200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:129091800-129108800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:129092600-129109200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr7:129093200-129109400	Weak transcription	Fetal Thymus	thymus
11	chr7:129093400-129134800	Weak transcription	Right Atrium	heart
12	chr7:129095200-129111800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:129095400-129109800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:129095400-129115000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:129096400-129109200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:129096800-129110200	Weak transcription	Small Intestine	intestine
17	chr7:129096800-129112000	Weak transcription	GM12878-XiMat	blood
18	chr7:129097200-129110200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:129097600-129128600	Weak transcription	NH-A	brain
20	chr7:129100400-129113000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:129101000-129109400	Weak transcription	Brain Angular Gyrus	brain
22	chr7:129101400-129109600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:129101600-129128600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr7:129102200-129124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:129102400-129120400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:129103000-129117400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:129103000-129141200	Weak transcription	Hela-S3	cervix
28	chr7:129103200-129110000	Weak transcription	Brain Hippocampus Middle	brain
29	chr7:129103200-129129600	Weak transcription	Dnd41	blood
30	chr7:129103200-129135400	Weak transcription	HepG2	liver
31	chr7:129104200-129141600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:129104400-129109600	Weak transcription	NHLF	lung
33	chr7:129104800-129109000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr7:129104800-129109400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr7:129104800-129112000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr7:129104800-129121200	Weak transcription	Fetal Stomach	stomach
37	chr7:129105000-129108600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr7:129105400-129127400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr7:129106000-129108800	Genic enhancers	HSMM	muscle
40	chr7:129106400-129108600	Enhancers	NHDF-Ad	bronchial
41	chr7:129106400-129108800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:129106600-129108600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr7:129106600-129108800	Enhancers	Osteobl	bone
44	chr7:129106600-129109400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:129106600-129121400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:129106800-129108800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:129106800-129108800	Genic enhancers	Fetal Heart	heart
48	chr7:129106800-129109600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr7:129107000-129110000	Weak transcription	Psoas Muscle	Psoas
50	chr7:129107000-129110800	Weak transcription	Fetal Muscle Leg	muscle

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