Variant report

Variant	rs12078104
Chromosome Location	chr1:161733327-161733328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr1:161733166-161733760	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr1:161733125-161733797	HCT-116	colon:	n/a	n/a
3	CTCF	chr1:161733293-161733601	A549	lung:	n/a	n/a
4	RAD21	chr1:161733196-161733721	A549	lung:	n/a	n/a
5	JUND	chr1:161733233-161733819	HCT-116	colon:	n/a	n/a
6	CTCF	chr1:161733286-161733653	GM12878	blood:	n/a	n/a
7	SMC3	chr1:161733305-161733647	Hela-S3	cervix:	n/a	n/a
8	STAT3	chr1:161733302-161733555	MCF10A-Er-Src	breast:	n/a	n/a
9	RCOR1	chr1:161733313-161733598	K562	blood:	n/a	n/a
10	RAD21	chr1:161733253-161733705	A549	lung:	n/a	n/a
11	GTF3C2	chr1:161733278-161733670	Hela-S3	cervix:	n/a	n/a
12	MYC	chr1:161733313-161733660	MCF10A-Er-Src	breast:	n/a	n/a
13	RAD21	chr1:161733312-161733573	SK-N-SH_RA	brain:	n/a	n/a
14	E2F4	chr1:161733325-161733611	MCF10A-Er-Src	breast:	n/a	n/a
15	RFX5	chr1:161733325-161733660	Hela-S3	cervix:	n/a	n/a
16	RAD21	chr1:161733306-161733652	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr1:161733303-161733568	GM12878	blood:	n/a	n/a
18	RAD21	chr1:161733317-161733617	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr1:161733286-161733631	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr1:161733317-161733593	SK-N-SH_RA	brain:	n/a	n/a
21	RAD21	chr1:161733313-161733651	HepG2	liver:	n/a	n/a
22	RAD21	chr1:161733292-161733577	HepG2	liver:	n/a	n/a
23	CTCF	chr1:161733265-161733669	HepG2	liver:	n/a	n/a
24	SMC3	chr1:161733311-161733648	HepG2	liver:	n/a	n/a
25	CTCF	chr1:161733291-161733654	IMR90	lung:	n/a	n/a
26	RAD21	chr1:161733268-161733612	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr1:161733190-161733665	MCF-7	breast:	n/a	n/a
28	RAD21	chr1:161733218-161733802	HCT-116	colon:	n/a	n/a
29	CBX3	chr1:161733233-161733786	HCT-116	colon:	n/a	n/a
30	CBX3	chr1:161733294-161733674	K562	blood:	n/a	n/a
31	CTCF	chr1:161732977-161733929	A549	lung:	n/a	n/a
32	CTCF	chr1:161733167-161733759	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr1:161733181-161733778	HCT-116	colon:	n/a	n/a
34	CTCF	chr1:161733220-161733370	HAc	cerebellar:	n/a	n/a
35	CTCF	chr1:161733252-161733570	MCF-7	breast:	n/a	n/a
36	RCOR1	chr1:161733325-161733653	Hela-S3	cervix:	n/a	n/a
37	RAD21	chr1:161733254-161733714	HepG2	liver:	n/a	n/a
38	CTCF	chr1:161733032-161733806	HCT-116	colon:	n/a	n/a
39	SMC3	chr1:161733316-161733568	K562	blood:	n/a	n/a
40	CTCF	chr1:161733297-161733673	K562	blood:	n/a	n/a
41	CTCF	chr1:161733229-161733731	A549	lung:	n/a	n/a
42	RAD21	chr1:161733268-161733709	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161718558..161723568-chr1:161731521..161737462,16	K562	blood:
2	chr1:161718568..161724937-chr1:161732191..161738837,13	K562	blood:
3	chr1:161733009..161733606-chr1:161762222..161762733,2	MCF-7	breast:
4	chr1:161732981..161734219-chr1:162006454..162007424,4	MCF-7	breast:
5	chr1:161727932..161729878-chr1:161731559..161734430,3	K562	blood:
6	chr1:161718595..161726705-chr1:161728119..161739561,22	MCF-7	breast:

No data

Variant related genes	Relation type
ATF6	TF binding region
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10399867	0.80[ASN][1000 genomes]
rs10436881	0.85[CHB][hapmap]
rs1063179	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10917835	1.00[GIH][hapmap]
rs10917867	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10917876	0.85[CHB][hapmap]
rs10918029	0.92[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12042663	0.82[ASN][1000 genomes]
rs12086247	0.85[CHB][hapmap]
rs12097712	0.87[ASN][1000 genomes]
rs12691498	0.92[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12728760	0.91[ASN][1000 genomes]
rs60578284	0.87[ASN][1000 genomes]
rs6657266	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6698956	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs73019308	0.91[ASN][1000 genomes]
rs7355188	0.82[ASN][1000 genomes]
rs9970071	1.00[GIH][hapmap]

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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12078104	FCRLA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161720400-161734600	Weak transcription	Aorta	Aorta
2	chr1:161720600-161734600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:161720600-161734800	Weak transcription	Psoas Muscle	Psoas
4	chr1:161720600-161736000	Weak transcription	Spleen	Spleen
5	chr1:161720800-161734600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:161720800-161735000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:161720800-161735000	Weak transcription	Stomach Mucosa	stomach
8	chr1:161721000-161734600	Weak transcription	Right Ventricle	heart
9	chr1:161721000-161734600	Weak transcription	HSMMtube	muscle
10	chr1:161721000-161735000	Weak transcription	Fetal Heart	heart
11	chr1:161721200-161733800	Weak transcription	Pancreas	Pancrea
12	chr1:161721200-161734600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:161721200-161734800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:161723200-161734800	Weak transcription	Colonic Mucosa	Colon
15	chr1:161723400-161736000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:161724200-161735000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:161724600-161734600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:161724600-161734800	Weak transcription	Thymus	Thymus
19	chr1:161724600-161735000	Weak transcription	Fetal Brain Male	brain
20	chr1:161724600-161736000	Weak transcription	Small Intestine	intestine
21	chr1:161724800-161734600	Weak transcription	NHLF	lung
22	chr1:161724800-161736000	Weak transcription	Gastric	stomach
23	chr1:161725400-161733400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:161725400-161735000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:161725600-161733400	Weak transcription	HepG2	liver
26	chr1:161726000-161733600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:161726000-161734600	Weak transcription	Fetal Kidney	kidney
28	chr1:161726000-161735800	Weak transcription	Esophagus	oesophagus
29	chr1:161726600-161734600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:161726800-161734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:161726800-161734600	Weak transcription	NHEK	skin
32	chr1:161726800-161734800	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:161726800-161734800	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:161726800-161734800	Weak transcription	Fetal Lung	lung
35	chr1:161726800-161735000	Weak transcription	Primary T cells from cord blood	blood
36	chr1:161726800-161735000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:161726800-161735800	Weak transcription	Lung	lung
38	chr1:161727000-161734600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:161727000-161734600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:161727000-161735000	Weak transcription	Brain Substantia Nigra	brain
41	chr1:161727200-161734800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:161727200-161735000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:161727400-161733400	Weak transcription	A549	lung
44	chr1:161727400-161734400	Weak transcription	Primary B cells from cord blood	blood
45	chr1:161727400-161735000	Weak transcription	Brain Angular Gyrus	brain
46	chr1:161727400-161735000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:161727800-161734600	Weak transcription	Ovary	ovary
48	chr1:161727800-161735000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:161728000-161734600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:161728000-161734600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links