Variant report

Variant	rs1146640
Chromosome Location	chr1:76259469-76259470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:62)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:62 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
2	POLR2A	chr1:76257436-76260415	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:76258715-76259846	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr1:76257827-76264091	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:76259093-76259809	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:76259378-76259550	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:76258688-76260442	U87	brain:	n/a	n/a
8	POLR2A	chr1:76258458-76259893	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:76258496-76259591	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:76258323-76260083	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
12	POLR2A	chr1:76258370-76259639	K562	blood:	n/a	n/a
13	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr1:76259288-76260045	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
16	POLR2A	chr1:76257031-76260129	K562	blood:	n/a	n/a
17	POLR2A	chr1:76257887-76264164	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:76259306-76259579	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:76259323-76259674	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:76257762-76263752	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr1:76258682-76259568	K562	blood:	n/a	n/a
22	POLR2A	chr1:76259145-76259507	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:76258764-76263332	GM19099	blood:	n/a	n/a
24	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:76259117-76259767	GM12892	blood:	n/a	n/a
26	POLR2A	chr1:76259238-76259639	GM12891	blood:	n/a	n/a
27	POLR2A	chr1:76259208-76259589	GM12891	blood:	n/a	n/a
28	POLR2A	chr1:76258457-76260407	K562	blood:	n/a	n/a
29	POLR2A	chr1:76258771-76259648	GM12891	blood:	n/a	n/a
30	POLR2A	chr1:76259372-76259683	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:76259304-76259562	HCT-116	colon:	n/a	n/a
32	POLR2A	chr1:76258323-76260040	GM12892	blood:	n/a	n/a
33	POLR2A	chr1:76250047-76263901	GM18505	blood:	n/a	n/a
34	POLR2A	chr1:76249945-76266639	GM12891	blood:	n/a	n/a
35	POLR2A	chr1:76259276-76260086	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr1:76257798-76260132	K562	blood:	n/a	n/a
37	POLR2A	chr1:76258687-76260408	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr1:76250036-76264085	K562	blood:	n/a	n/a
39	POLR2A	chr1:76257881-76260036	A549	lung:	n/a	n/a
40	POLR2A	chr1:76258504-76260115	GM12892	blood:	n/a	n/a
41	POLR2A	chr1:76259191-76259872	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr1:76258280-76259660	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr1:76259106-76259730	PBDE	blood:	n/a	n/a
44	POLR2A	chr1:76256643-76264175	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:76259072-76264143	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr1:76258745-76260239	U87	brain:	n/a	n/a
47	POLR2A	chr1:76258838-76259617	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr1:76257012-76263648	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr1:76258882-76259610	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr1:76257332-76260436	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76252156..76254487-chr1:76258379..76261694,3	MCF-7	breast:
2	chr1:75819174..75821466-chr1:76259462..76262137,2	K562	blood:
3	chr1:76257416..76260329-chr1:76260481..76263578,4	MCF-7	breast:
4	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
5	chr1:76188764..76194417-chr1:76259356..76264333,14	K562	blood:
6	chr1:76196771..76198499-chr1:76258126..76260501,2	K562	blood:
7	chr1:76196771..76202637-chr1:76258126..76262356,7	K562	blood:

No data

Variant related genes	Relation type
MSH4	TF binding region
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000207241	Chromatin interaction
ENSG00000057468	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1021463	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1068884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10747330	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10873726	1.00[EUR][1000 genomes]
rs10873786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1093007	1.00[EUR][1000 genomes]
rs1093010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11161785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11161801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1144330	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1144332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1144335	1.00[EUR][1000 genomes]
rs1146575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146578	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146585	1.00[EUR][1000 genomes]
rs1146586	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146589	1.00[EUR][1000 genomes]
rs1146595	1.00[EUR][1000 genomes]
rs1146596	1.00[EUR][1000 genomes]
rs1146597	1.00[EUR][1000 genomes]
rs1146599	1.00[EUR][1000 genomes]
rs1146600	1.00[EUR][1000 genomes]
rs1146601	1.00[EUR][1000 genomes]
rs1146604	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146621	1.00[EUR][1000 genomes]
rs1146633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1250879	1.00[EUR][1000 genomes]
rs1251066	1.00[EUR][1000 genomes]
rs1251074	1.00[EUR][1000 genomes]
rs1251271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1251532	1.00[EUR][1000 genomes]
rs1251538	1.00[EUR][1000 genomes]
rs1251554	1.00[EUR][1000 genomes]
rs1251559	1.00[EUR][1000 genomes]
rs1251563	1.00[EUR][1000 genomes]
rs1251585	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1251589	1.00[EUR][1000 genomes]
rs1251590	1.00[EUR][1000 genomes]
rs1251592	1.00[EUR][1000 genomes]
rs1251593	1.00[EUR][1000 genomes]
rs1469988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1565718	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1565719	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1591119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1616175	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1658743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1694408	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1694423	1.00[EUR][1000 genomes]
rs1759276	1.00[AMR][1000 genomes]
rs1770514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1770884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796825	1.00[YRI][hapmap]
rs1873895	1.00[AMR][1000 genomes]
rs211714	1.00[EUR][1000 genomes]
rs211720	1.00[EUR][1000 genomes]
rs211734	1.00[EUR][1000 genomes]
rs211735	1.00[EUR][1000 genomes]
rs211738	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs211739	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2347963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3119821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs381183	1.00[EUR][1000 genomes]
rs392695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs445008	1.00[EUR][1000 genomes]
rs699684	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs699685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs699686	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs699687	1.00[EUR][1000 genomes]
rs699688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs699689	1.00[EUR][1000 genomes]
rs699823	1.00[EUR][1000 genomes]
rs699826	1.00[EUR][1000 genomes]
rs7541791	1.00[EUR][1000 genomes]
rs814846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs814852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs814854	1.00[EUR][1000 genomes]
rs815300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs815302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs815312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs865263	1.00[AMR][1000 genomes]
rs9437227	1.00[EUR][1000 genomes]
rs946982	1.00[EUR][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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 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	chr1:76254000-76260000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:76254200-76263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:76254400-76262400	Strong transcription	Placenta	Placenta
4	chr1:76254400-76265200	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:76254800-76262400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:76254800-76262600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:76255200-76261400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:76255200-76263600	Strong transcription	Fetal Lung	lung
9	chr1:76255400-76262600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:76255400-76263000	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr1:76255400-76265200	Weak transcription	Right Atrium	heart
12	chr1:76255600-76263000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:76255600-76264000	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr1:76255800-76261600	Weak transcription	Fetal Heart	heart
15	chr1:76255800-76264000	Strong transcription	Brain Anterior Caudate	brain
16	chr1:76255800-76264200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:76255800-76264200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:76255800-76264400	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:76256000-76262400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:76256000-76262800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:76256000-76264200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:76256000-76264200	Strong transcription	Fetal Thymus	thymus
23	chr1:76256000-76264400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:76256000-76264400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:76256000-76264600	Strong transcription	Fetal Stomach	stomach
26	chr1:76256200-76259600	Strong transcription	Lung	lung
27	chr1:76256200-76262600	Strong transcription	Fetal Kidney	kidney
28	chr1:76256200-76263000	Strong transcription	Ovary	ovary
29	chr1:76256400-76259600	Strong transcription	HSMMtube	muscle
30	chr1:76256400-76262400	Strong transcription	Fetal Brain Female	brain
31	chr1:76256400-76262800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:76256400-76262800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:76256400-76264400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:76256600-76261600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:76256600-76262400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:76256600-76262600	Strong transcription	Primary B cells from cord blood	blood
37	chr1:76256600-76262600	Strong transcription	HMEC	breast
38	chr1:76256600-76263000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:76256600-76263000	Strong transcription	Colon Smooth Muscle	Colon
40	chr1:76256600-76263200	Strong transcription	Brain Angular Gyrus	brain
41	chr1:76256600-76263200	Strong transcription	Rectal Smooth Muscle	rectum
42	chr1:76256600-76263200	Strong transcription	NHLF	lung
43	chr1:76256600-76263400	Strong transcription	Adipose Nuclei	Adipose
44	chr1:76256600-76263400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr1:76256600-76264000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr1:76256600-76264000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:76256600-76264200	Strong transcription	Brain Cingulate Gyrus	brain
48	chr1:76256600-76264600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr1:76256600-76265000	Strong transcription	Primary T cells from cord blood	blood
50	chr1:76256800-76259600	Weak transcription	Stomach Mucosa	stomach

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