Variant report

Variant	rs3752619
Chromosome Location	chr7:127221134-127221135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127204431..127206594-chr7:127219494..127222300,2	MCF-7	breast:
2	chr7:126985391..126987885-chr7:127220985..127222536,2	MCF-7	breast:
3	7:127009457-127018926..7:127216013-127221502	GM12878	blood:
4	chr7:127200505..127203389-chr7:127219797..127221382,2	K562	blood:
5	chr7:127030414..127032802-chr7:127220953..127224227,3	K562	blood:

Variant related genes	Relation type
ENSG00000048405	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10487494	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12536698	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs12706803	0.86[ASN][1000 genomes]
rs13235029	0.86[ASN][1000 genomes]
rs13244426	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13247976	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1419408	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs17660187	1.00[JPT][hapmap]
rs2272374	1.00[JPT][hapmap]
rs33973710	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34121113	0.86[ASN][1000 genomes]
rs34195583	0.86[ASN][1000 genomes]
rs34211107	0.93[ASN][1000 genomes]
rs34365152	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34388330	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34599926	0.89[ASN][1000 genomes]
rs34814259	0.86[ASN][1000 genomes]
rs35144279	0.86[ASN][1000 genomes]
rs35528098	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757785	1.00[JPT][hapmap]
rs3808111	1.00[JPT][hapmap]
rs3808115	1.00[JPT][hapmap]
rs62468943	0.93[ASN][1000 genomes]
rs62483172	0.93[ASN][1000 genomes]
rs6957054	0.86[ASN][1000 genomes]
rs6964793	0.93[ASN][1000 genomes]
rs746238	1.00[JPT][hapmap]
rs7811506	0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3752619	LRRC4	cis	parietal	SCAN
rs3752619	HYAL4	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127200600-127221400	Weak transcription	Pancreas	Pancrea
2	chr7:127203600-127221400	Weak transcription	Left Ventricle	heart
3	chr7:127209600-127221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:127210200-127221600	Weak transcription	Small Intestine	intestine
5	chr7:127212800-127221400	Weak transcription	Spleen	Spleen
6	chr7:127213000-127221200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:127213400-127221400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:127214600-127222000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:127215000-127222000	Strong transcription	Fetal Muscle Leg	muscle
10	chr7:127215200-127221200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:127215200-127221200	Weak transcription	HMEC	breast
12	chr7:127215200-127221400	Weak transcription	Fetal Intestine Small	intestine
13	chr7:127215800-127221200	Weak transcription	Gastric	stomach
14	chr7:127216200-127222000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:127216800-127221200	Weak transcription	HUVEC	blood vessel
16	chr7:127216800-127222200	Weak transcription	Stomach Mucosa	stomach
17	chr7:127217000-127221200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:127217200-127221200	Weak transcription	Ovary	ovary
19	chr7:127217600-127221400	Strong transcription	Fetal Thymus	thymus
20	chr7:127218000-127221600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr7:127218000-127221800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr7:127218000-127222000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:127218000-127222000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:127218000-127222200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:127218000-127222800	Weak transcription	Hela-S3	cervix
26	chr7:127218000-127223000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr7:127218000-127223200	Strong transcription	Primary B cells from cord blood	blood
28	chr7:127218000-127223400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:127218000-127223400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr7:127218200-127221200	Weak transcription	Fetal Lung	lung
31	chr7:127218200-127221400	Weak transcription	Fetal Kidney	kidney
32	chr7:127218200-127221600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:127218200-127223200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:127218200-127223600	Strong transcription	Primary hematopoietic stem cells	blood
35	chr7:127218200-127223600	Strong transcription	Fetal Intestine Large	intestine
36	chr7:127218200-127223800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:127218400-127221200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:127218400-127222200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr7:127218600-127221200	Weak transcription	A549	lung
40	chr7:127218600-127222000	Weak transcription	Right Ventricle	heart
41	chr7:127218800-127223400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:127219000-127223400	Strong transcription	K562	blood
43	chr7:127219200-127221200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:127219200-127221200	Weak transcription	HSMMtube	muscle
45	chr7:127219200-127221400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr7:127219200-127223600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr7:127219400-127221200	Strong transcription	HSMM	muscle
48	chr7:127219400-127221200	Weak transcription	NHLF	lung
49	chr7:127219400-127221400	Weak transcription	Brain Hippocampus Middle	brain
50	chr7:127219400-127221400	Weak transcription	Lung	lung

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