Variant report

Variant	rs11971358
Chromosome Location	chr7:6769299-6769300
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	POLR2A	chr7:6769072-6770050	GM19193	blood:	n/a	n/a
2	GTF2F1	chr7:6769215-6769578	K562	blood:	n/a	n/a
3	MTA3	chr7:6768884-6770122	GM12878	blood:	n/a	n/a
4	SIN3A	chr7:6769057-6770204	H1-hESC	embryonic stem cell:	n/a	chr7:6769397-6769408
5	POLR2A	chr7:6768936-6770212	SK-N-MC	brain:	n/a	n/a
6	RCOR1	chr7:6769146-6769594	K562	blood:	n/a	n/a
7	TAF1	chr7:6769259-6769571	GM12891	blood:	n/a	n/a
8	SIX5	chr7:6769218-6769507	A549	lung:	n/a	n/a
9	GABPA	chr7:6768978-6769671	A549	lung:	n/a	chr7:6769390-6769401 chr7:6769392-6769401 chr7:6769355-6769369 chr7:6769390-6769404
10	POLR2A	chr7:6768948-6770053	GM18505	blood:	n/a	n/a
11	CBX3	chr7:6768880-6769635	K562	blood:	n/a	n/a
12	NRF1	chr7:6768971-6769967	SK-N-SH	brain:	n/a	chr7:6769390-6769401 chr7:6769392-6769401 chr7:6769358-6769369 chr7:6769355-6769369 chr7:6769389-6769400 chr7:6769390-6769404
13	EP300	chr7:6769082-6769557	HepG2	liver:	n/a	chr7:6769342-6769349
14	JUND	chr7:6769127-6769570	HepG2	liver:	n/a	n/a
15	NR2F2	chr7:6769016-6769807	MCF-7	breast:	n/a	n/a
16	RXRA	chr7:6768841-6769861	HepG2	liver:	n/a	chr7:6768960-6768969 chr7:6769350-6769357
17	CTCF	chr7:6769180-6769330	GM06990	blood:	n/a	n/a
18	PAX5	chr7:6768848-6769607	GM12878	blood:	n/a	chr7:6768960-6768969
19	MAX	chr7:6769162-6769596	H1-hESC	embryonic stem cell:	n/a	n/a
20	GABPA	chr7:6769196-6769573	HepG2	liver:	n/a	chr7:6769390-6769401 chr7:6769392-6769401 chr7:6769355-6769369 chr7:6769390-6769404
21	IRF4	chr7:6768988-6769599	GM12878	blood:	n/a	n/a
22	MAX	chr7:6769168-6769768	MCF-7	breast:	n/a	n/a
23	CHD1	chr7:6769255-6769940	GM12878	blood:	n/a	n/a
24	ZNF143	chr7:6769088-6769501	K562	blood:	n/a	chr7:6769268-6769278 chr7:6769326-6769344
25	CREB1	chr7:6769086-6769579	H1-hESC	embryonic stem cell:	n/a	n/a
26	TBP	chr7:6769169-6769597	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr7:6768932-6769632	HepG2	liver:	n/a	n/a
28	MXI1	chr7:6769069-6770133	GM12878	blood:	n/a	n/a
29	YY1	chr7:6769035-6769547	H1-hESC	embryonic stem cell:	n/a	n/a
30	ETS1	chr7:6769044-6769578	GM12878	blood:	n/a	chr7:6769341-6769350 chr7:6769339-6769349 chr7:6769338-6769353 chr7:6769340-6769353 chr7:6769338-6769354 chr7:6769341-6769350 chr7:6769341-6769350 chr7:6769341-6769350 chr7:6769341-6769350 chr7:6769341-6769350 chr7:6769341-6769350
31	MAX	chr7:6769128-6769754	ECC-1	luminal epithelium:	n/a	n/a
32	KAP1	chr7:6769081-6769700	HEK293	kidney:	n/a	n/a
33	POU2F2	chr7:6768846-6769657	GM12878	blood:	n/a	n/a
34	BRCA1	chr7:6769210-6769550	Hela-S3	cervix:	n/a	n/a
35	SETDB1	chr7:6769066-6769528	K562	blood:	n/a	chr7:6769277-6769301
36	SETDB1	chr7:6769143-6769422	U2OS	brain:	n/a	chr7:6769277-6769301
37	HEY1	chr7:6768853-6769957	HepG2	liver:	n/a	n/a
38	REST	chr7:6769080-6769648	PANC-1	pancreas:	n/a	n/a
39	ELF1	chr7:6769027-6769689	HepG2	liver:	n/a	chr7:6769400-6769409 chr7:6769340-6769353
40	POLR2A	chr7:6768933-6769626	HepG2	liver:	n/a	n/a
41	POLR2A	chr7:6768951-6770528	GM12892	blood:	n/a	n/a
42	POLR2A	chr7:6768989-6769686	HCT-116	colon:	n/a	n/a
43	CTCF	chr7:6769236-6769388	Lung_OC	lung:	n/a	n/a
44	CREB1	chr7:6769195-6769646	A549	lung:	n/a	n/a
45	POLR2A	chr7:6769103-6769656	MCF10A-Er-Src	breast:	n/a	n/a
46	CTCF	chr7:6769160-6769310	NB4	blood:	n/a	n/a
47	POLR2A	chr7:6769047-6769689	HepG2	liver:	n/a	n/a
48	CBX3	chr7:6768879-6769361	K562	blood:	n/a	n/a
49	CTCF	chr7:6769216-6769318	GM19238	blood:	n/a	n/a
50	NRF1	chr7:6769197-6769557	HepG2	liver:	n/a	chr7:6769390-6769401 chr7:6769392-6769401 chr7:6769358-6769369 chr7:6769355-6769369 chr7:6769389-6769400 chr7:6769390-6769404

No.	Distal block	Cell Line	Cell type
1	chr7:6745463..6748475-chr7:6767656..6769994,3	K562	blood:
2	chr7:6746161..6747688-chr7:6768318..6771249,2	MCF-7	breast:
3	chr7:6768428..6771621-chr7:6773707..6775724,3	MCF-7	breast:
4	chr7:6616941..6618678-chr7:6767339..6769412,2	MCF-7	breast:
5	chr7:6048395..6048947-chr7:6768981..6769924,2	NB4	blood:
6	chr7:6675529..6677980-chr7:6768487..6770695,2	K562	blood:
7	chr2:85554880..85555877-chr7:6769205..6770035,2	Hela-S3	cervix:
8	chr7:6744871..6747873-chr7:6767656..6771321,4	K562	blood:
9	chr7:6767588..6769922-chr7:6774691..6777140,2	MCF-7	breast:
10	chr7:6745224..6747442-chr7:6767898..6770902,3	MCF-7	breast:
11	chr7:6766860..6769459-chr7:6864426..6866111,2	MCF-7	breast:

Variant related genes	Relation type
PMS2CL	TF binding region
ENSG00000136247	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000146574	Chromatin interaction
ENSG00000187953	Chromatin interaction
ENSG00000164631	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000205903	Chromatin interaction
ENSG00000106305	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11974014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11975128	1.00[CHB][hapmap]
rs11975963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979742	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979883	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2346236	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55667244	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57608899	1.00[ASN][1000 genomes]
rs59433350	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59436190	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59660422	1.00[ASN][1000 genomes]
rs60111824	1.00[ASN][1000 genomes]
rs6463577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6945312	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6950034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950197	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73331249	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73333108	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73333121	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv887439	chr7:6736332-6791749	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015646	chr7:6738483-6779270	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv887440	chr7:6743097-6820508	Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv887441	chr7:6744957-6919214	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	esv1819001	chr7:6746810-6785602	Weak transcription Enhancers Flanking Active TSS Active TSS 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	12 gene(s)	inside rSNPs	diseases
7	nsv966755	chr7:6750289-6769785	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv966754	chr7:6750289-6838266	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers 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	9 gene(s)	inside rSNPs	diseases
9	nsv887442	chr7:6753286-6820508	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv887443	chr7:6753286-6832265	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv887444	chr7:6753286-6855510	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv887445	chr7:6758018-6843722	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv887446	chr7:6758018-6870635	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv887447	chr7:6764583-6843722	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv887448	chr7:6764583-6855510	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv887449	chr7:6764583-6870635	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	esv2757207	chr7:6764583-6977214	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
18	esv2759504	chr7:6764583-6977214	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6768200-6770600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:6768400-6769400	Flanking Active TSS	GM12878-XiMat	blood
3	chr7:6768600-6769400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:6768600-6769400	Active TSS	Brain Germinal Matrix	brain
5	chr7:6768600-6769400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
6	chr7:6768600-6770000	Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr7:6768600-6770000	Active TSS	Brain Cingulate Gyrus	brain
8	chr7:6768600-6770000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr7:6768600-6770000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:6768600-6770000	Active TSS	Brain Substantia Nigra	brain
11	chr7:6768600-6770000	Active TSS	Right Ventricle	heart
12	chr7:6768600-6770200	Active TSS	Duodenum Mucosa	Duodenum
13	chr7:6768600-6770200	Active TSS	Fetal Heart	heart
14	chr7:6768600-6770200	Active TSS	Stomach Smooth Muscle	stomach
15	chr7:6768600-6770400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr7:6768600-6770400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr7:6768600-6770400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:6768600-6770400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr7:6768600-6770400	Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr7:6768600-6770400	Active TSS	Brain Anterior Caudate	brain
21	chr7:6768600-6770400	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr7:6768600-6770600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:6768600-6770600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr7:6768600-6770600	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr7:6768600-6770600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:6768600-6770600	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr7:6768600-6770600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:6768600-6770600	Active TSS	Brain Angular Gyrus	brain
29	chr7:6768600-6770600	Active TSS	Brain Hippocampus Middle	brain
30	chr7:6768600-6770600	Active TSS	Colon Smooth Muscle	Colon
31	chr7:6768600-6770600	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr7:6768600-6770600	Active TSS	Fetal Intestine Small	intestine
33	chr7:6768600-6770800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr7:6768600-6770800	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr7:6768600-6770800	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr7:6768600-6770800	Active TSS	Fetal Brain Female	brain
37	chr7:6768600-6770800	Active TSS	HSMM	muscle
38	chr7:6768600-6771000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr7:6768600-6771000	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr7:6768600-6771000	Active TSS	Rectal Smooth Muscle	rectum
41	chr7:6768800-6769400	Active TSS	Adipose Nuclei	Adipose
42	chr7:6768800-6769400	Flanking Active TSS	Dnd41	blood
43	chr7:6768800-6770000	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr7:6768800-6770600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:6768800-6770600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:6768800-6770600	Active TSS	Fetal Intestine Large	intestine
47	chr7:6768800-6770600	Active TSS	Fetal Kidney	kidney
48	chr7:6768800-6770600	Active TSS	Thymus	Thymus
49	chr7:6768800-6771000	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr7:6769000-6769400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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