Variant report

Variant	rs7742824
Chromosome Location	chr6:44065311-44065312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:44064707..44066979-chr6:44078095..44080647,3	MCF-7	breast:
2	chr6:44063788..44067397-chr6:44214255..44217581,5	MCF-7	breast:
3	chr6:44059285..44062949-chr6:44063714..44068721,8	K562	blood:
4	chr6:44064352..44066624-chr6:44094843..44096793,3	K562	blood:
5	chr6:44064487..44065451-chr6:44119305..44119965,4	K562	blood:
6	chr6:44063271..44067340-chr6:44221821..44225276,4	MCF-7	breast:
7	chr6:44064455..44066858-chr6:44120767..44125089,3	MCF-7	breast:
8	chr6:44026454..44027963-chr6:44063940..44066196,2	K562	blood:
9	chr6:44064491..44067269-chr6:44068919..44074061,5	MCF-7	breast:
10	chr6:44064308..44065554-chr6:44205339..44206301,3	MCF-7	breast:
11	chr6:44063799..44065316-chr6:44213671..44216377,2	MCF-7	breast:
12	chr6:44064116..44065383-chr6:44119168..44120496,12	MCF-7	breast:
13	chr6:44063441..44066080-chr6:44220225..44222286,2	K562	blood:
14	chr6:44063516..44066397-chr6:44271609..44273554,2	K562	blood:
15	chr6:44064110..44066569-chr6:44222530..44225900,6	K562	blood:
16	chr6:44064723..44067197-chr6:44214028..44217115,4	K562	blood:
17	chr6:44064144..44068096-chr6:44213556..44216776,6	K562	blood:
18	chr6:44064536..44066199-chr6:44223382..44226796,3	MCF-7	breast:
19	chr6:44063761..44065519-chr6:44068411..44070135,2	K562	blood:
20	chr6:44064146..44065473-chr6:44305968..44306588,4	K562	blood:
21	chr6:44064908..44068117-chr6:44068233..44072672,4	MCF-7	breast:
22	chr6:44047147..44049384-chr6:44064492..44067747,3	K562	blood:
23	chr6:44064372..44068377-chr6:44222364..44225900,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137216	Chromatin interaction
ENSG00000265700	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000180992	Chromatin interaction
ENSG00000157593	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10085205	0.87[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs2096199	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4610558	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55934950	0.85[ASN][1000 genomes]
rs56168551	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57139546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57576544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59842359	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60105057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60207481	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs66629131	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935537	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73429745	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7742030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752653	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755223	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7773700	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462935	chr6:44046143-44117607	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv603002	chr6:44046143-44117607	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Major depressive disorder	23377640	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7742824	MRPL14	Cis_1M	lymphoblastoid	RTeQTL
rs7742824	KLHDC3	cis	parietal	SCAN
rs7742824	SLC22A7	cis	cerebellum	SCAN
rs7742824	TMEM63B	cis	cerebellum	SCAN
rs7742824	MRPL14	cis	Liver	GTEx
rs7742824	CDC5L	cis	parietal	SCAN
rs7742824	MRPL14	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44044200-44067000	Weak transcription	NHDF-Ad	bronchial
2	chr6:44044600-44067600	Weak transcription	Spleen	Spleen
3	chr6:44044800-44067000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:44044800-44067400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr6:44044800-44070200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:44044800-44071400	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:44045000-44067400	Weak transcription	Brain Anterior Caudate	brain
8	chr6:44045000-44071800	Weak transcription	Aorta	Aorta
9	chr6:44045600-44067000	Weak transcription	Fetal Brain Female	brain
10	chr6:44047000-44066600	Weak transcription	Thymus	Thymus
11	chr6:44047400-44067200	Weak transcription	Dnd41	blood
12	chr6:44047400-44067400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr6:44047400-44067600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:44047400-44069200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:44047400-44071400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:44049400-44067000	Weak transcription	GM12878-XiMat	blood
17	chr6:44051600-44067400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:44052600-44067000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:44052600-44071000	Weak transcription	HSMMtube	muscle
20	chr6:44052800-44067000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:44052800-44067400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:44052800-44071000	Weak transcription	Placenta	Placenta
23	chr6:44052800-44071800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:44053000-44067000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:44053000-44067000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:44053000-44070400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:44054800-44067400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:44055000-44068000	Weak transcription	Esophagus	oesophagus
29	chr6:44055200-44067600	Weak transcription	Fetal Lung	lung
30	chr6:44055200-44068000	Weak transcription	Gastric	stomach
31	chr6:44055200-44068000	Weak transcription	Right Atrium	heart
32	chr6:44055400-44067000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:44055400-44067200	Weak transcription	A549	lung
34	chr6:44055400-44067400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:44055400-44067400	Weak transcription	HSMM	muscle
36	chr6:44055400-44067600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:44055400-44067800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:44055400-44067800	Weak transcription	Osteobl	bone
39	chr6:44055400-44068000	Weak transcription	Left Ventricle	heart
40	chr6:44055400-44069800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:44055400-44071400	Weak transcription	HMEC	breast
42	chr6:44055400-44071800	Weak transcription	Psoas Muscle	Psoas
43	chr6:44055600-44066000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:44055600-44067000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:44055600-44072200	Weak transcription	NH-A	brain
46	chr6:44055800-44067000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:44055800-44071400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:44055800-44076000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:44055800-44078800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:44056200-44078400	Weak transcription	Fetal Kidney	kidney

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