Variant report

Variant	rs3823946
Chromosome Location	chr7:27823017-27823018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:27701152..27704360-chr7:27822065..27825517,3	K562	blood:
2	chr7:27815094..27816615-chr7:27822533..27825294,2	K562	blood:
3	chr7:27822809..27825747-chr7:27834000..27835827,2	K562	blood:
4	chr7:27818847..27822042-chr7:27822389..27826371,4	K562	blood:
5	chr7:27822572..27826113-chr7:27831204..27834771,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106049	Chromatin interaction
ENSG00000106052	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12164139	0.84[CEU][hapmap]
rs13247833	0.84[AFR][1000 genomes]
rs17155705	0.90[LWK][hapmap];0.90[YRI][hapmap]
rs17155836	0.81[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2237342	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34526836	0.83[AFR][1000 genomes]
rs35645888	0.89[AFR][1000 genomes]
rs3779472	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs66610237	0.86[AFR][1000 genomes]
rs6961429	0.88[CEU][hapmap]
rs723699	0.88[CEU][hapmap]
rs723700	0.88[CEU][hapmap]
rs73073391	0.89[AFR][1000 genomes]
rs7455882	0.88[CEU][hapmap]
rs7794292	0.88[CEU][hapmap]

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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3823946	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL
rs3823946	SNX10	cis	cerebellum	SCAN
rs3823946	GHRHR	cis	cerebellum	SCAN
rs3823946	TAX1BP1	cis	cerebellum	SCAN
rs3823946	SCRN1	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27781000-27861800	Weak transcription	Aorta	Aorta
2	chr7:27784800-27834000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:27784800-27878400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:27785000-27825000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:27787600-27825000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:27787800-27826600	Weak transcription	Small Intestine	intestine
7	chr7:27790600-27825000	Weak transcription	NHLF	lung
8	chr7:27790600-27835000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:27790600-27857400	Weak transcription	Colonic Mucosa	Colon
10	chr7:27792200-27825000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr7:27792200-27825000	Weak transcription	Brain Hippocampus Middle	brain
12	chr7:27792800-27825200	Weak transcription	Lung	lung
13	chr7:27798600-27847800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:27798600-27874000	Weak transcription	Brain Angular Gyrus	brain
15	chr7:27801200-27825200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:27801200-27851800	Weak transcription	Fetal Brain Male	brain
17	chr7:27801400-27831400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:27801400-27838400	Weak transcription	Fetal Brain Female	brain
19	chr7:27801600-27852800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:27801800-27825200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:27802800-27826200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:27804600-27824400	Weak transcription	Fetal Intestine Small	intestine
23	chr7:27805800-27825200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr7:27805800-27832200	Weak transcription	Fetal Stomach	stomach
25	chr7:27805800-27857600	Weak transcription	Esophagus	oesophagus
26	chr7:27806000-27882600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:27806400-27825000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:27806400-27878600	Weak transcription	Right Ventricle	heart
29	chr7:27806600-27825200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr7:27806600-27827800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr7:27810200-27825000	Weak transcription	HepG2	liver
32	chr7:27810400-27831600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:27810400-27831600	Weak transcription	Colon Smooth Muscle	Colon
34	chr7:27810600-27824800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:27810800-27831600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:27811000-27825000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:27811200-27832200	Weak transcription	Ovary	ovary
38	chr7:27811200-27833600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:27811400-27825000	Weak transcription	Fetal Kidney	kidney
40	chr7:27811400-27825000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr7:27811400-27825200	Weak transcription	Fetal Muscle Leg	muscle
42	chr7:27811400-27825200	Weak transcription	Thymus	Thymus
43	chr7:27811400-27831200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:27811600-27824800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:27811600-27824800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:27811600-27827600	Weak transcription	Fetal Lung	lung
47	chr7:27811800-27824400	Weak transcription	Fetal Thymus	thymus
48	chr7:27811800-27831400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr7:27811800-27835000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:27812000-27824600	Weak transcription	Dnd41	blood

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