Variant report

Variant	rs9660185
Chromosome Location	chr1:173832101-173832102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:214)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:214 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:173830742-173838152	GM18951	blood:	n/a	n/a
2	POLR2A	chr1:173830604-173834319	HL-60	blood:	n/a	n/a
3	POLR2A	chr1:173831251-173832299	Gliobla	brain:	n/a	n/a
4	POLR2A	chr1:173829652-173834370	K562	blood:	n/a	n/a
5	RUNX3	chr1:173831750-173832214	GM12878	blood:	n/a	n/a
6	GTF2F1	chr1:173831954-173832405	H1-hESC	embryonic stem cell:	n/a	n/a
7	RCOR1	chr1:173831939-173832682	Hela-S3	cervix:	n/a	n/a
8	TCF7L2	chr1:173831413-173832431	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:173828332-173838242	K562	blood:	n/a	n/a
10	PBX3	chr1:173830728-173832741	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr1:173831238-173832410	GM12878	blood:	n/a	n/a
12	CEBPD	chr1:173830788-173832895	K562	blood:	n/a	n/a
13	MAX	chr1:173831836-173832203	Hela-S3	cervix:	n/a	n/a
14	BCLAF1	chr1:173831688-173832909	K562	blood:	n/a	chr1:173831994-173832003
15	CEBPB	chr1:173831805-173832399	A549	lung:	n/a	chr1:173832102-173832113 chr1:173832103-173832114 chr1:173832102-173832115
16	ZBTB33	chr1:173831654-173832175	HCT-116	colon:	n/a	n/a
17	POLR2A	chr1:173829381-173833686	GM12891	blood:	n/a	n/a
18	POLR2A	chr1:173825088-173838434	K562	blood:	n/a	n/a
19	POLR2A	chr1:173827997-173836225	HepG2	liver:	n/a	n/a
20	CCNT2	chr1:173831768-173832913	K562	blood:	n/a	chr1:173832018-173832027
21	POLR2A	chr1:173830571-173832892	GM12891	blood:	n/a	n/a
22	POLR2A	chr1:173830687-173832742	Raji	blood:	n/a	n/a
23	STAT5A	chr1:173831559-173832855	GM12878	blood:	n/a	chr1:173832020-173832032 chr1:173831994-173832005 chr1:173832018-173832030
24	TAF7	chr1:173831606-173832341	K562	blood:	n/a	n/a
25	POLR2A	chr1:173829861-173834161	K562	blood:	n/a	n/a
26	POLR2A	chr1:173829985-173833751	GM19193	blood:	n/a	n/a
27	ELK1	chr1:173832080-173832992	K562	blood:	n/a	n/a
28	POLR2A	chr1:173824570-173837689	A549	lung:	n/a	n/a
29	POLR2A	chr1:173828233-173834504	GM12892	blood:	n/a	n/a
30	TEAD4	chr1:173831795-173832237	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:173830753-173833030	HCT-116	colon:	n/a	n/a
32	JUND	chr1:173830702-173832980	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr1:173829284-173838362	K562	blood:	n/a	n/a
34	POLR2A	chr1:173829132-173838052	PFSK-1	brain:	n/a	n/a
35	CHD1	chr1:173831798-173837941	IMR90	lung:	n/a	chr1:173836993-173837000 chr1:173837608-173837618 chr1:173837832-173837842
36	BCLAF1	chr1:173831672-173832655	GM12878	blood:	n/a	chr1:173831994-173832003
37	POLR2A	chr1:173829663-173838350	K562	blood:	n/a	n/a
38	POLR2A	chr1:173829737-173838261	PANC-1	pancreas:	n/a	n/a
39	FOSL2	chr1:173831577-173832347	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:173831314-173832276	MCF-7	breast:	n/a	n/a
41	PML	chr1:173831601-173832445	MCF-7	breast:	n/a	n/a
42	POLR2A	chr1:173829767-173838193	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:173829946-173832856	NB4	blood:	n/a	n/a
44	BCLAF1	chr1:173830668-173832603	GM12878	blood:	n/a	chr1:173831994-173832003
45	MTA3	chr1:173830550-173833227	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:173829033-173834330	U87	brain:	n/a	n/a
47	POLR2A	chr1:173829700-173838480	GM18505	blood:	n/a	n/a
48	MAFF	chr1:173831943-173832783	K562	blood:	n/a	n/a
49	HMGN3	chr1:173831761-173832386	K562	blood:	n/a	n/a
50	POLR2A	chr1:173830001-173838163	GM12892	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173831929..173834882-chr1:173882309..173883868,2	MCF-7	breast:
2	chr1:173829871..173833250-chr1:173884943..173888028,3	K562	blood:
3	chr1:173831705..173832255-chr17:7137439..7138382,2	Hela-S3	cervix:
4	chr1:173789792..173811494-chr1:173827886..173840273,103	K562	blood:
5	chr1:173831983..173832573-chr11:62388801..62389692,2	Hela-S3	cervix:
6	chr1:173831314..173839948-chr1:173984831..173993131,14	MCF-7	breast:
7	chr1:173831168..173832165-chr16:1822973..1823541,2	Hela-S3	cervix:
8	chr1:173682439..173685635-chr1:173828531..173832401,4	MCF-7	breast:
9	chr1:173831906..173839548-chr1:173987374..173993282,15	MCF-7	breast:
10	chr1:173793576..173795606-chr1:173831172..173833639,2	MCF-7	breast:
11	chr1:173789473..173804179-chr1:173828884..173842109,95	K562	blood:
12	chr1:173445658..173447676-chr1:173831376..173834939,3	K562	blood:
13	chr1:173682967..173685869-chr1:173831317..173832954,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SERPINC1-1	chr1:173827684-173834420	NONHSAT007659

No data

Variant related genes	Relation type
GAS5-AS1	TF binding region
ENSG00000076321	Chromatin interaction
ENSG00000117601	Chromatin interaction
ENSG00000074071	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000236535	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000004975	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000197774	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12117115	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137553	0.89[CEU][hapmap];1.00[GIH][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138617	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746886	0.93[AMR][1000 genomes]
rs12749768	1.00[ASN][1000 genomes]
rs34997480	1.00[ASN][1000 genomes]
rs35872531	1.00[ASN][1000 genomes]
rs55762016	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 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	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
2	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
3	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
4	chr1:173794800-173834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:173818600-173834800	Strong transcription	Fetal Muscle Leg	muscle
7	chr1:173818600-173834800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:173819200-173833200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:173819200-173833800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:173819200-173834000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:173819400-173834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:173819600-173834000	Strong transcription	Fetal Thymus	thymus
13	chr1:173819600-173835600	Strong transcription	Fetal Muscle Trunk	muscle
14	chr1:173820600-173833800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:173820600-173834000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:173821000-173834000	Strong transcription	Liver	Liver
17	chr1:173821000-173834000	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr1:173822000-173834000	Strong transcription	Fetal Intestine Large	intestine
19	chr1:173822400-173832600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:173822400-173833600	Strong transcription	Fetal Brain Female	brain
21	chr1:173822400-173833800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:173822800-173832400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:173822800-173832400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:173822800-173833400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:173822800-173834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:173823000-173835000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:173823200-173833400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:173823400-173832200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:173824600-173833800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:173824800-173834600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr1:173825200-173832200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:173825600-173832400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:173826800-173832200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:173827000-173832200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:173827000-173833800	Weak transcription	HepG2	liver
36	chr1:173827400-173832200	Weak transcription	HSMM	muscle
37	chr1:173827400-173832600	Weak transcription	Fetal Kidney	kidney
38	chr1:173827400-173834400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:173827600-173832200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:173827600-173832200	Weak transcription	Hela-S3	cervix
41	chr1:173827600-173832200	Weak transcription	HSMMtube	muscle
42	chr1:173827600-173832200	Weak transcription	NHDF-Ad	bronchial
43	chr1:173827600-173833400	Strong transcription	Fetal Intestine Small	intestine
44	chr1:173827600-173834000	Weak transcription	Psoas Muscle	Psoas
45	chr1:173827800-173834400	Strong transcription	Fetal Stomach	stomach
46	chr1:173828000-173832200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:173828000-173832200	Weak transcription	Primary B cells from cord blood	blood
48	chr1:173828600-173832200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:173828600-173833200	Strong transcription	Dnd41	blood
50	chr1:173829000-173832600	Strong transcription	Adipose Nuclei	Adipose

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