Variant report

Variant	rs552937143
Chromosome Location	chr7:39662514-39662515
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr7:39662445-39663523	SK-N-SH_RA	brain:	n/a	chr7:39662807-39662826 chr7:39663473-39663482 chr7:39663474-39663485 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39663477-39663488 chr7:39663495-39663504 chr7:39663498-39663507 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39663476-39663485 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
2	JUND	chr7:39662456-39663323	H1-hESC	embryonic stem cell:	n/a	chr7:39663142-39663151 chr7:39663137-39663146
3	MAX	chr7:39662446-39663940	ECC-1	luminal epithelium:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
4	YY1	chr7:39662460-39663694	GM12892	blood:	n/a	chr7:39662807-39662826 chr7:39663473-39663482 chr7:39663474-39663485 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39663477-39663488 chr7:39663495-39663504 chr7:39663644-39663655 chr7:39663498-39663507 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39663476-39663485 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
5	BHLHE40	chr7:39662312-39664819	GM12878	blood:	n/a	chr7:39663497-39663513 chr7:39663776-39663792 chr7:39663770-39663786 chr7:39663467-39663483
6	YY1	chr7:39662425-39663472	GM12878	blood:	n/a	chr7:39662807-39662826 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
7	YY1	chr7:39662440-39663868	HepG2	liver:	n/a	chr7:39662807-39662826 chr7:39663473-39663482 chr7:39663474-39663485 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39663477-39663488 chr7:39663495-39663504 chr7:39663644-39663655 chr7:39663498-39663507 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39663476-39663485 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
8	MXI1	chr7:39662425-39662716	K562	blood:	n/a	n/a
9	POU2F2	chr7:39662457-39663439	GM12878	blood:	n/a	chr7:39663142-39663154
10	POLR2A	chr7:39662408-39663414	GM12891	blood:	n/a	n/a
11	MAZ	chr7:39662486-39663522	HepG2	liver:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
12	MXI1	chr7:39662512-39663825	HepG2	liver:	n/a	n/a
13	EBF1	chr7:39662438-39662831	GM12878	blood:	n/a	chr7:39662689-39662700
14	TCF7L2	chr7:39662393-39663887	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr7:39662475-39663875	HepG2	liver:	n/a	n/a
16	ZNF384	chr7:39662208-39662550	K562	blood:	n/a	n/a
17	STAT1	chr7:39662485-39662700	GM12878	blood:	n/a	n/a
18	MXI1	chr7:39662169-39663832	GM12878	blood:	n/a	n/a
19	MAX	chr7:39662383-39663972	SK-N-SH	brain:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
20	EP300	chr7:39662267-39662783	GM12878	blood:	n/a	n/a
21	GTF2F1	chr7:39662360-39663365	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr7:39662305-39663855	NB4	blood:	n/a	n/a
23	MAX	chr7:39662369-39663902	NB4	blood:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
24	REST	chr7:39662205-39664044	H1-neurons	neurons:	n/a	chr7:39663136-39663149 chr7:39662958-39662976 chr7:39663151-39663161
25	POLR2A	chr7:39661358-39663450	K562	blood:	n/a	n/a
26	POLR2A	chr7:39661360-39663434	K562	blood:	n/a	n/a
27	POLR2A	chr7:39662492-39663494	HCT-116	colon:	n/a	n/a
28	POLR2A	chr7:39661961-39663605	U87	brain:	n/a	n/a
29	POLR2A	chr7:39662259-39663436	GM12892	blood:	n/a	n/a
30	HEY1	chr7:39662472-39663464	K562	blood:	n/a	chr7:39663124-39663139 chr7:39662955-39662964
31	POLR2A	chr7:39659839-39663493	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr7:39662431-39663371	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr7:39662434-39663810	MCF-7	breast:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
34	POLR2A	chr7:39660809-39665213	IMR90	lung:	n/a	n/a
35	MAX	chr7:39662470-39663430	ECC-1	luminal epithelium:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
36	POLR2A	chr7:39661586-39663615	PANC-1	pancreas:	n/a	n/a
37	TBP	chr7:39662271-39663350	GM12878	blood:	n/a	n/a
38	WRNIP1	chr7:39661909-39662848	GM12878	blood:	n/a	n/a
39	TAF1	chr7:39662491-39663493	K562	blood:	n/a	n/a
40	POLR2A	chr7:39662381-39663725	ProgFib	skin:	n/a	n/a
41	TAF1	chr7:39662416-39663437	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr7:39661268-39663897	GM12878	blood:	n/a	n/a
43	HCFC1	chr7:39662409-39665997	Hela-S3	cervix:	n/a	n/a
44	GABPA	chr7:39662271-39663736	MCF-7	breast:	n/a	n/a
45	ATF2	chr7:39662511-39663130	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr7:39662499-39663765	Gliobla	brain:	n/a	n/a
47	MAX	chr7:39662383-39663901	HepG2	liver:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
48	YY1	chr7:39662495-39663361	A549	lung:	n/a	chr7:39662807-39662826 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
49	POLR2A	chr7:39662335-39663548	GM12892	blood:	n/a	n/a
50	POLR2A	chr7:39662445-39663824	GM18951	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:39662467-39662517	HRCEpiC	kidney:	n/a
2	chr7:39662467-39662517	ovcar-3	ovarian:	n/a
3	chr7:39662467-39662517	K562	blood:	n/a
4	chr7:39662467-39662517	ECC-1	luminal epithelium:	n/a
5	chr7:39662467-39662517	HepG2	liver:	n/a
6	chr7:39662467-39662517	GM06990	blood:	n/a
7	chr7:39662467-39662517	AG10803	skin:	n/a
8	chr7:39662467-39662517	HUVEC	blood vessel:	n/a
9	chr7:39662467-39662517	BJ	skin:	n/a
10	chr7:39662467-39662517	HCT-116	colon:	n/a
11	chr7:39662467-39662517	PrEC	prostate:	n/a
12	chr7:39662467-39662517	GM12878	blood:	n/a
13	chr7:39662467-39662517	GM19239	blood:	n/a
14	chr7:39662467-39662517	MCF10A-Er-Src	breast:	n/a
15	chr7:39662467-39662517	BE2_C	brain:	n/a
16	chr7:39662467-39662517	NH-A	brain:	n/a
17	chr7:39662467-39662517	SK-N-MC	brain:	n/a
18	chr7:39662467-39662517	HRE	kidney:	n/a
19	chr7:39662467-39662517	GM12892	blood:	n/a
20	chr7:39662467-39662517	U87	brain:	n/a
21	chr7:39662467-39662517	Hepatocyte	liver:	n/a
22	chr7:39662467-39662517	HEEpiC	esophagus:	n/a
23	chr7:39662467-39662517	T-47D	breast:	n/a
24	chr7:39662467-39662517	AG04449	skin:	fetal
25	chr7:39662467-39662517	AG04450	lung:	fetal
26	chr7:39662467-39662517	PFSK-1	brain:	n/a
27	chr7:39662467-39662517	HPAEpiC	pulmonary alveolar:	n/a
28	chr7:39662467-39662517	ProgFib	skin:	n/a
29	chr7:39662467-39662517	IMR90	lung:	fetal
30	chr7:39662467-39662517	NT2-D1	testis:	n/a
31	chr7:39662467-39662517	NHDF-neo	bronchial:	n/a
32	chr7:39662467-39662517	NHBE	bronchial:	n/a
33	chr7:39662467-39662517	NB4	blood:	n/a
34	chr7:39662467-39662517	Caco-2	colon:	n/a
35	chr7:39662467-39662517	Hela-S3	cervix:	n/a
36	chr7:39662467-39662517	SKMC	muscle:	n/a
37	chr7:39662467-39662517	H1-hESC	embryonic stem cell:	embryo
38	chr7:39662467-39662517	PANC-1	pancreas:	n/a
39	chr7:39662467-39662517	Jurkat	blood:	n/a
40	chr7:39662467-39662517	MCF-7	breast:	n/a
41	chr7:39662467-39662517	HIPEpiC	eye:	n/a
42	chr7:39662467-39662517	SAEC	small airway:	n/a
43	chr7:39662467-39662517	A549	lung:	n/a
44	chr7:39662467-39662517	LNCaP	prostate:	n/a
45	chr7:39662467-39662517	AoSMC	blood vessel:	n/a
46	chr7:39662467-39662517	GM12891	blood:	n/a
47	chr7:39662467-39662517	HRPEpiC	eye:	n/a
48	chr7:39662467-39662517	SK-N-SH	brain:	n/a
49	chr7:39662467-39662517	HNPCEpiC	eye:	n/a
50	chr7:39662467-39662517	HL-60	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:39616830..39619300-chr7:39660316..39662885,2	K562	blood:
2	chr7:39649814..39652615-chr7:39661583..39664092,3	MCF-7	breast:
3	chr7:39652942..39654975-chr7:39661144..39662912,2	MCF-7	breast:
4	chr7:39661595..39664442-chr7:39724184..39727170,2	MCF-7	breast:
5	chr7:39661404..39663086-chr7:39725958..39728030,2	MCF-7	breast:
6	chr7:39603623..39606050-chr7:39662280..39665105,2	MCF-7	breast:
7	chr7:39660516..39662861-chr7:39772033..39774524,2	K562	blood:
8	chr17:56735362..56737542-chr7:39660335..39663097,2	MCF-7	breast:
9	chr7:39661332..39663000-chr7:39732479..39734683,2	K562	blood:
10	chr7:39660619..39666370-chr7:39771379..39777121,13	MCF-7	breast:
11	chr7:39635256..39637997-chr7:39660350..39662905,2	MCF-7	breast:
12	chr7:39643128..39644638-chr7:39660434..39662671,2	MCF-7	breast:
13	chr7:39661063..39664836-chr7:39769831..39775766,6	MCF-7	breast:

Variant related genes	Relation type
RALA	TF binding region
RALA	CpG island
ENSG00000227172	Chromatin interaction
ENSG00000188185	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000006451	Chromatin interaction
ENSG00000241127	Chromatin interaction
ENSG00000231951	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39661200-39662600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr7:39661200-39662800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
3	chr7:39661400-39662600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:39661400-39662800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:39661400-39662800	Flanking Active TSS	NH-A	brain
6	chr7:39661600-39662600	Flanking Active TSS	Dnd41	blood
7	chr7:39661600-39662600	Flanking Active TSS	K562	blood
8	chr7:39661600-39662800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:39661600-39663000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr7:39661600-39664600	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr7:39661800-39662600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:39661800-39662600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:39661800-39662600	Flanking Active TSS	HSMM	muscle
14	chr7:39661800-39662600	Flanking Active TSS	HSMMtube	muscle
15	chr7:39661800-39662800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr7:39661800-39664400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr7:39661800-39664600	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr7:39662000-39662600	Flanking Active TSS	Liver	Liver
19	chr7:39662000-39662600	Active TSS	Brain Germinal Matrix	brain
20	chr7:39662000-39662600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr7:39662000-39662600	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr7:39662000-39662600	Flanking Active TSS	Fetal Intestine Small	intestine
23	chr7:39662000-39662600	Flanking Active TSS	Hela-S3	cervix
24	chr7:39662000-39662600	Flanking Active TSS	Osteobl	bone
25	chr7:39662000-39662800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr7:39662000-39662800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr7:39662000-39662800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:39662000-39662800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:39662000-39662800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:39662000-39662800	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr7:39662000-39664200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr7:39662000-39664200	Active TSS	A549	lung
33	chr7:39662000-39664400	Active TSS	H9 Cell Line	embryonic stem cell
34	chr7:39662000-39664400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr7:39662000-39664600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr7:39662000-39665200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr7:39662200-39662600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr7:39662200-39662600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr7:39662200-39662600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr7:39662200-39662600	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr7:39662200-39662600	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr7:39662200-39662600	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr7:39662200-39662600	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr7:39662200-39662600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr7:39662200-39662600	Flanking Active TSS	Fetal Brain Female	brain
46	chr7:39662200-39662600	Flanking Active TSS	Fetal Kidney	kidney
47	chr7:39662200-39662600	Flanking Active TSS	Fetal Stomach	stomach
48	chr7:39662200-39662600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr7:39662200-39662600	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr7:39662200-39662600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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