Variant report

Variant	rs1403525
Chromosome Location	chr3:43063406-43063407
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43062963..43065859-chr3:43071110..43073966,2	K562	blood:
2	chr3:43047918..43050087-chr3:43062104..43064961,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10470680	1.00[ASN][1000 genomes]
rs10510736	0.82[YRI][hapmap]
rs12629332	1.00[CHB][hapmap]
rs1392319	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074894	1.00[ASN][1000 genomes]
rs1816227	1.00[ASN][1000 genomes]
rs28378297	1.00[ASN][1000 genomes]
rs28601753	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655956	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673478	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915020	1.00[ASN][1000 genomes]
rs489117	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs530842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs534284	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs551658	1.00[CHB][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs604393	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs61004728	1.00[ASN][1000 genomes]
rs617014	1.00[ASN][1000 genomes]
rs62248962	1.00[ASN][1000 genomes]
rs62249006	1.00[ASN][1000 genomes]
rs62249007	1.00[ASN][1000 genomes]
rs62249008	1.00[ASN][1000 genomes]
rs62249009	1.00[ASN][1000 genomes]
rs62249011	1.00[ASN][1000 genomes]
rs62249013	1.00[ASN][1000 genomes]
rs62249014	1.00[ASN][1000 genomes]
rs62249015	0.86[EUR][1000 genomes]
rs62249016	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249584	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651899	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6763762	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6773223	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6775999	1.00[ASN][1000 genomes]
rs678310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6794402	0.81[YRI][hapmap]
rs6798412	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6798520	0.80[CEU][hapmap]
rs680967	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs681341	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73075297	1.00[ASN][1000 genomes]
rs73075301	1.00[ASN][1000 genomes]
rs73077208	1.00[ASN][1000 genomes]
rs73077214	1.00[ASN][1000 genomes]
rs73077238	1.00[ASN][1000 genomes]
rs735320	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73832423	1.00[ASN][1000 genomes]
rs73832424	1.00[ASN][1000 genomes]
rs7617715	1.00[ASN][1000 genomes]
rs7625959	0.82[TSI][hapmap]
rs7641452	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7643433	0.85[YRI][hapmap]
rs7644923	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs834579	0.82[TSI][hapmap]
rs834584	0.82[TSI][hapmap]
rs9311330	1.00[ASN][1000 genomes]
rs9311331	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9808932	1.00[ASN][1000 genomes]
rs9815609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816391	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824700	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833284	1.00[ASN][1000 genomes]
rs9837761	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852930	1.00[ASN][1000 genomes]
rs9858270	1.00[ASN][1000 genomes]
rs9862469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865715	1.00[CHB][hapmap]
rs9870478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv460523	chr3:43025986-43063406	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv590150	chr3:43025986-43063406	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv432417	chr3:43045796-43098296	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1403525	HIGD1A	cis	cerebellum	SCAN
rs1403525	HHATL	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43053600-43073200	Weak transcription	Right Atrium	heart
2	chr3:43059600-43074400	Weak transcription	Lung	lung
3	chr3:43059600-43084600	Weak transcription	Pancreas	Pancrea
4	chr3:43059800-43064200	Enhancers	Fetal Brain Male	brain
5	chr3:43059800-43064800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:43059800-43065200	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr3:43060200-43065200	Enhancers	Fetal Thymus	thymus
8	chr3:43060200-43065400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:43060200-43065400	Enhancers	Thymus	Thymus
10	chr3:43060600-43064600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:43060600-43064800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:43060800-43063800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:43060800-43065400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr3:43060800-43069600	Weak transcription	Stomach Mucosa	stomach
15	chr3:43061000-43065000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:43061000-43065400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:43061000-43066200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:43061000-43072200	Weak transcription	Liver	Liver
19	chr3:43061000-43080200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:43061200-43063600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:43061400-43064600	Enhancers	Primary T cells from cord blood	blood
22	chr3:43061400-43064600	Enhancers	Dnd41	blood
23	chr3:43061600-43065400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:43061800-43064800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:43061800-43073000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:43062000-43063800	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr3:43062200-43064600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:43062200-43065200	Strong transcription	Placenta	Placenta
29	chr3:43062600-43064800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr3:43062800-43063600	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr3:43063000-43064400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:43063000-43077400	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:43063200-43064000	Enhancers	Colon Smooth Muscle	Colon
34	chr3:43063400-43063800	Enhancers	Adipose Nuclei	Adipose
35	chr3:43063400-43065000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:43063400-43065400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr3:43063400-43072000	Weak transcription	Stomach Smooth Muscle	stomach

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