Variant report

Variant	rs340630
Chromosome Location	chr4:87958395-87958396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87855920..87858337-chr4:87956894..87959736,2	K562	blood:
2	chr4:87944684..87947564-chr4:87957551..87959550,2	MCF-7	breast:
3	chr4:87952663..87956832-chr4:87958320..87961763,4	K562	blood:
4	chr4:87947975..87950419-chr4:87957844..87960013,2	K562	blood:
5	chr4:87926892..87929968-chr4:87957011..87960890,5	K562	blood:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10015639	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10032244	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11729622	0.87[ASN][1000 genomes]
rs12651081	0.90[LWK][hapmap]
rs13126334	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13127250	0.88[ASN][1000 genomes]
rs1471251	0.82[CEU][hapmap]
rs2007132	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2053769	0.84[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2053770	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28495007	0.83[EUR][1000 genomes]
rs3113494	0.81[LWK][hapmap]
rs340626	0.99[ASN][1000 genomes]
rs340633	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs340636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs340637	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs340638	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs340639	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs340641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs340642	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs340643	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340648	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340650	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs340651	0.86[ASN][1000 genomes]
rs375795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4274814	0.85[LWK][hapmap]
rs443459	0.99[ASN][1000 genomes]
rs4536898	0.85[LWK][hapmap]
rs4693798	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4693800	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58633957	0.99[ASN][1000 genomes]
rs6531941	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs6531946	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811587	0.90[ASN][1000 genomes]
rs6839933	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs867196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9715807	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Systemic lupus erythematosus	22291604	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs340630	AFF1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87944200-87960800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr4:87944800-87961600	Enhancers	Fetal Heart	heart
3	chr4:87949200-87961000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:87949400-87960600	Enhancers	Liver	Liver
5	chr4:87949600-87960800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr4:87949800-87960800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr4:87950000-87958600	Enhancers	Psoas Muscle	Psoas
8	chr4:87950000-87960200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:87950200-87962600	Enhancers	Fetal Muscle Leg	muscle
10	chr4:87951600-87959000	Enhancers	Fetal Intestine Large	intestine
11	chr4:87951800-87960400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:87952400-87960000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:87952400-87960400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr4:87952400-87967000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr4:87952600-87958800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:87952600-87961000	Enhancers	K562	blood
17	chr4:87952600-87968000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:87952800-87961000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:87953000-87960800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:87953400-87958800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:87953400-87965800	Weak transcription	Primary T cells from cord blood	blood
22	chr4:87953400-87967600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:87953600-87960600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:87953600-87961000	Enhancers	Fetal Lung	lung
25	chr4:87953800-87958800	Enhancers	Ovary	ovary
26	chr4:87953800-87958800	Enhancers	Right Atrium	heart
27	chr4:87953800-87959800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:87953800-87961600	Enhancers	Brain Substantia Nigra	brain
29	chr4:87953800-87963600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:87954000-87958600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:87954000-87959000	Enhancers	Placenta	Placenta
32	chr4:87954000-87959000	Enhancers	Left Ventricle	heart
33	chr4:87954200-87960000	Enhancers	Brain Cingulate Gyrus	brain
34	chr4:87954400-87958600	Enhancers	Duodenum Mucosa	Duodenum
35	chr4:87954400-87959600	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr4:87954600-87959600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:87954600-87959600	Enhancers	NHDF-Ad	bronchial
38	chr4:87954600-87961200	Enhancers	Adipose Nuclei	Adipose
39	chr4:87954600-87961600	Enhancers	Brain Angular Gyrus	brain
40	chr4:87954600-87962200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr4:87954600-87963400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:87954600-87965800	Enhancers	Colon Smooth Muscle	Colon
43	chr4:87954800-87961000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:87955000-87958600	Enhancers	Lung	lung
45	chr4:87955000-87958800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:87955200-87959800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr4:87955400-87959200	Weak transcription	Brain Germinal Matrix	brain
48	chr4:87955400-87959600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:87955400-87960200	Enhancers	Brain Hippocampus Middle	brain
50	chr4:87955400-87960800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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