Variant report

Variant	rs6865
Chromosome Location	chr3:42826041-42826042
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42821893..42823608-chr3:42825720..42828571,2	K562	blood:
2	chr3:42825664..42827247-chr3:42863922..42866111,2	MCF-7	breast:
3	chr3:42824804..42827092-chr3:42834818..42838109,3	K562	blood:
4	chr3:42796446..42798021-chr3:42824548..42826746,2	K562	blood:
5	chr3:42825788..42828570-chr3:42866080..42867830,2	K562	blood:
6	chr3:42820160..42826427-chr3:42842009..42849039,11	K562	blood:
7	chr3:42824890..42826427-chr3:42846368..42849039,2	K562	blood:

Variant related genes	Relation type
ENSG00000144648	Chromatin interaction
ENSG00000181061	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10470680	1.00[ASN][1000 genomes]
rs123506	1.00[CHB][hapmap]
rs123509	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs1392319	1.00[ASN][1000 genomes]
rs17074894	1.00[ASN][1000 genomes]
rs17238972	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1816227	1.00[ASN][1000 genomes]
rs28378297	1.00[ASN][1000 genomes]
rs28601753	1.00[ASN][1000 genomes]
rs339661	1.00[CHB][hapmap]
rs339682	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap]
rs339683	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap]
rs339686	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs3915020	1.00[ASN][1000 genomes]
rs4404423	1.00[CHB][hapmap]
rs551658	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs61004728	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]
rs62249016	1.00[ASN][1000 genomes]
rs62249584	1.00[ASN][1000 genomes]
rs6763762	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6773223	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6775999	1.00[ASN][1000 genomes]
rs6782601	0.90[MEX][hapmap]
rs6798412	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs73075297	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73075301	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077208	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077214	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077220	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73077238	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73085343	1.00[ASN][1000 genomes]
rs73087348	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735320	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7617715	1.00[ASN][1000 genomes]
rs7641452	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs7644923	1.00[ASN][1000 genomes]
rs834579	1.00[CHD][hapmap]
rs834584	1.00[CHD][hapmap]
rs9311330	1.00[ASN][1000 genomes]
rs9311331	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9808932	1.00[ASN][1000 genomes]
rs9816391	1.00[ASN][1000 genomes]
rs9824700	1.00[ASN][1000 genomes]
rs9828785	1.00[ASN][1000 genomes]
rs9832875	0.90[MEX][hapmap]
rs9833284	1.00[ASN][1000 genomes]
rs9837761	1.00[ASN][1000 genomes]
rs9852930	1.00[ASN][1000 genomes]
rs9858270	1.00[ASN][1000 genomes]
rs9862469	1.00[ASN][1000 genomes]
rs9865715	1.00[CHB][hapmap]

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	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv236207	chr3:42825586-42829088	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv979823	chr3:42825813-42826813	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6865	HIGD1A	cis	parietal	SCAN
rs6865	SEC22C	cis	lymphoblastoid	seeQTL
rs6865	HHATL	cis	parietal	SCAN
rs6865	HHATL	cis	cerebellum	SCAN
rs6865	HIGD1A	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42814800-42840800	Weak transcription	Spleen	Spleen
2	chr3:42815000-42834800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:42815200-42827000	Weak transcription	Fetal Lung	lung
4	chr3:42815200-42828200	Weak transcription	Fetal Intestine Small	intestine
5	chr3:42815200-42834800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:42815200-42834800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:42815200-42834800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:42815200-42834800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:42815200-42834800	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:42815200-42834800	Weak transcription	Ovary	ovary
11	chr3:42815200-42834800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:42815200-42834800	Weak transcription	A549	lung
13	chr3:42815200-42835200	Weak transcription	Right Ventricle	heart
14	chr3:42815200-42836400	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:42815200-42837400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:42815200-42842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:42815200-42842200	Weak transcription	Aorta	Aorta
18	chr3:42815200-42842400	Weak transcription	Psoas Muscle	Psoas
19	chr3:42815400-42826800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:42815400-42826800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:42815400-42827400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:42815400-42827600	Weak transcription	Primary B cells from cord blood	blood
23	chr3:42815400-42832400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:42815400-42833600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:42815400-42834400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:42815400-42834800	Weak transcription	Brain Germinal Matrix	brain
27	chr3:42815400-42837200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:42815400-42844000	Weak transcription	NHDF-Ad	bronchial
29	chr3:42815600-42827600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:42815600-42841800	Weak transcription	Thymus	Thymus
31	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:42816200-42837600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:42820400-42834800	Weak transcription	HSMMtube	muscle
35	chr3:42821200-42826200	Weak transcription	Hela-S3	cervix
36	chr3:42821400-42828400	Strong transcription	Dnd41	blood
37	chr3:42821400-42837400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:42821800-42827000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:42821800-42834800	Weak transcription	Esophagus	oesophagus
40	chr3:42821800-42834800	Weak transcription	Pancreas	Pancrea
41	chr3:42822000-42841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:42822400-42826800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:42822400-42826800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:42822400-42834800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:42822400-42834800	Weak transcription	NHLF	lung
46	chr3:42822400-42837200	Weak transcription	Brain Angular Gyrus	brain
47	chr3:42822400-42843400	Weak transcription	Small Intestine	intestine
48	chr3:42822800-42826400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:42822800-42826400	Weak transcription	Osteobl	bone
50	chr3:42822800-42827000	Weak transcription	Muscle Satellite Cultured Cells	--

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