Variant report

Variant	rs434350
Chromosome Location	chr6:5136219-5136220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:180)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:180 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:5136067-5136336	K562	blood:	n/a	n/a
2	CTCF	chr6:5136120-5136270	AG10803	skin:	n/a	n/a
3	CTCF	chr6:5136120-5136270	K562	blood:	n/a	n/a
4	CTCF	chr6:5136105-5136314	MCF-7	breast:	n/a	n/a
5	CTCF	chr6:5136120-5136270	SK-N-SH_RA	brain:	n/a	n/a
6	CTCF	chr6:5135987-5136397	GM12878	blood:	n/a	n/a
7	CTCF	chr6:5136100-5136250	GM12801	blood:	n/a	n/a
8	CTCF	chr6:5136140-5136290	HEK293	kidney:	n/a	n/a
9	CTCF	chr6:5136120-5136270	GM06990	blood:	n/a	n/a
10	CTCF	chr6:5136117-5136277	GM12891	blood:	n/a	n/a
11	CTCF	chr6:5136100-5136250	WI-38	lung:	n/a	n/a
12	CTCF	chr6:5136120-5136270	HPAF	blood vessel:	n/a	n/a
13	RAD21	chr6:5136047-5136368	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr6:5136100-5136250	MCF-7	breast:	n/a	n/a
15	CTCF	chr6:5136120-5136270	GM12867	blood:	n/a	n/a
16	CTCF	chr6:5136153-5136251	LNCaP	prostate:	n/a	n/a
17	CTCF	chr6:5136013-5136382	K562	blood:	n/a	n/a
18	CTCF	chr6:5136080-5136230	GM12866	blood:	n/a	n/a
19	CTCF	chr6:5136140-5136290	A549	lung:	n/a	n/a
20	CTCF	chr6:5136104-5136272	Pancreas_OC	pancreas:	n/a	n/a
21	CTCF	chr6:5136122-5136307	MCF-7	breast:	n/a	n/a
22	RAD21	chr6:5135892-5136390	HCT-116	colon:	n/a	n/a
23	CTCF	chr6:5136100-5136250	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr6:5136108-5136290	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr6:5136160-5136310	GM12875	blood:	n/a	n/a
26	CTCF	chr6:5136100-5136250	GM12865	blood:	n/a	n/a
27	CTCF	chr6:5136160-5136310	GM12868	blood:	n/a	n/a
28	RAD21	chr6:5136038-5136373	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr6:5136100-5136250	AG10803	skin:	n/a	n/a
30	CTCF	chr6:5136140-5136290	GM12874	blood:	n/a	n/a
31	CTCF	chr6:5136120-5136270	HEK293	kidney:	n/a	n/a
32	CTCF	chr6:5136048-5136289	Lung_OC	lung:	n/a	n/a
33	CTCF	chr6:5136120-5136270	HVMF	connective:	n/a	n/a
34	RAD21	chr6:5135976-5136410	ECC-1	luminal epithelium:	n/a	n/a
35	CTCF	chr6:5136100-5136250	HRPEpiC	eye:	n/a	n/a
36	YY1	chr6:5136069-5136339	K562	blood:	n/a	n/a
37	RAD21	chr6:5136047-5136377	SK-N-SH_RA	brain:	n/a	n/a
38	CTCF	chr6:5136120-5136270	BE2_C	brain:	n/a	n/a
39	CTCF	chr6:5136120-5136270	HMEC	breast:	n/a	n/a
40	CTCF	chr6:5136120-5136270	HUVEC	blood vessel:	n/a	n/a
41	CTCF	chr6:5136120-5136270	HFF	foreskin:	n/a	n/a
42	CTCF	chr6:5136160-5136310	GM06990	blood:	n/a	n/a
43	RAD21	chr6:5135998-5136368	HepG2	liver:	n/a	n/a
44	CTCF	chr6:5136067-5136323	GM12878	blood:	n/a	n/a
45	CTCF	chr6:5136085-5136318	SK-N-SH_RA	brain:	n/a	n/a
46	CTCF	chr6:5136140-5136290	HAc	cerebellar:	n/a	n/a
47	CTCF	chr6:5136120-5136270	GM12871	blood:	n/a	n/a
48	CTCF	chr6:5136021-5136479	MCF-7	breast:	n/a	n/a
49	RAD21	chr6:5135998-5136470	MCF-7	breast:	n/a	n/a
50	CTCF	chr6:5136140-5136290	AG09309	skin:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5056866..5057674-chr6:5135884..5136820,3	MCF-7	breast:
2	chr6:5135691..5136262-chr6:5402310..5402817,2	K562	blood:

No data

Variant related genes	Relation type
LYRM4	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10458182	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484846	1.00[ASN][1000 genomes]
rs11242990	1.00[ASN][1000 genomes]
rs11242991	1.00[ASN][1000 genomes]
rs12110634	1.00[ASN][1000 genomes]
rs12111219	1.00[ASN][1000 genomes]
rs12191255	1.00[ASN][1000 genomes]
rs12192863	1.00[ASN][1000 genomes]
rs12193229	1.00[ASN][1000 genomes]
rs12195956	1.00[ASN][1000 genomes]
rs12202160	1.00[ASN][1000 genomes]
rs12202384	1.00[ASN][1000 genomes]
rs12203248	1.00[ASN][1000 genomes]
rs12204382	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204490	1.00[ASN][1000 genomes]
rs12206931	1.00[ASN][1000 genomes]
rs12213584	1.00[ASN][1000 genomes]
rs13194957	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17139439	1.00[ASN][1000 genomes]
rs35400671	1.00[ASN][1000 genomes]
rs4959330	1.00[ASN][1000 genomes]
rs4959331	1.00[ASN][1000 genomes]
rs4960068	1.00[ASN][1000 genomes]
rs6597114	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597115	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911123	1.00[ASN][1000 genomes]
rs72811642	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811643	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761365	1.00[ASN][1000 genomes]
rs7757651	1.00[ASN][1000 genomes]
rs8980	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9405800	1.00[ASN][1000 genomes]
rs9504354	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
8	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
12	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
13	nsv5179	chr6:5121824-5167027	Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
15	esv3390320	chr6:5134378-5136926	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv3401138	chr6:5134553-5136701	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs434350	LYRM4	cis	multi-tissue	Pritchard
rs434350	LYRM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5129000-5136800	Weak transcription	Primary T cells from cord blood	blood
2	chr6:5129000-5162000	Weak transcription	K562	blood
3	chr6:5129800-5138000	Weak transcription	HepG2	liver
4	chr6:5130600-5140400	Weak transcription	Gastric	stomach
5	chr6:5130600-5172200	Weak transcription	Lung	lung
6	chr6:5130800-5139400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:5130800-5142400	Weak transcription	Fetal Intestine Small	intestine
8	chr6:5131000-5143000	Weak transcription	Spleen	Spleen
9	chr6:5132000-5139200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:5133200-5141800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:5133400-5136600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:5133400-5143200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:5133400-5143800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:5133400-5144000	Weak transcription	Fetal Brain Male	brain
15	chr6:5133400-5146000	Weak transcription	Psoas Muscle	Psoas
16	chr6:5133400-5151600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:5133600-5136600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:5133600-5143400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:5133600-5143800	Weak transcription	Fetal Stomach	stomach
20	chr6:5133800-5139200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:5133800-5139400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:5133800-5140000	Weak transcription	GM12878-XiMat	blood
23	chr6:5133800-5140600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:5133800-5142400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:5133800-5143000	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:5133800-5143400	Weak transcription	Left Ventricle	heart
27	chr6:5133800-5143600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:5133800-5153400	Weak transcription	Right Ventricle	heart
29	chr6:5134200-5139000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:5134200-5144200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:5134400-5139000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:5134400-5139000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr6:5134600-5138800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr6:5134600-5139000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:5134600-5139000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:5135000-5151000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:5135200-5139600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:5135200-5151800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:5135800-5136400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr6:5136000-5136400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:5136000-5136800	Enhancers	Primary B cells from peripheral blood	blood
42	chr6:5136200-5136400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:5136200-5136400	Enhancers	Adipose Nuclei	Adipose
44	chr6:5136200-5136400	Enhancers	Placenta	Placenta
45	chr6:5136200-5136400	Enhancers	NHEK	skin
46	chr6:5136200-5136600	Enhancers	HUVEC	blood vessel
47	chr6:5136200-5137000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr6:5136200-5139200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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