Variant report

Variant	rs2141698
Chromosome Location	chr2:173290395-173290396
allele	A/G
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	RAD21	chr2:173290092-173290475	H1-hESC	embryonic stem cell:	n/a	chr2:173290412-173290426
2	RAD21	chr2:173290123-173290408	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr2:173289913-173290435	HCT-116	colon:	n/a	chr2:173290412-173290426
4	CTCF	chr2:173290260-173290410	HMEC	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173290254..173291940-chr2:173293674..173296240,2	MCF-7	breast:
2	chr2:173145139..173147717-chr2:173288396..173290436,2	MCF-7	breast:

Variant related genes	Relation type
ITGA6	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs10930555	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583663	chr2:173287832-173307756	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv528899	chr2:173289239-173290395	Bivalent Enhancer Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv583664	chr2:173289239-173307756	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2141698	GJB6	trans	parietal	SCAN
rs2141698	MAP1D	cis	cerebellum	SCAN
rs2141698	SDC4	trans	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173285200-173291800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:173285200-173291800	Enhancers	Fetal Thymus	thymus
3	chr2:173286600-173290400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:173287600-173290600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:173287800-173291000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:173288200-173290400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:173288200-173290600	Weak transcription	Primary T cells from cord blood	blood
8	chr2:173288200-173290800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:173288400-173290400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:173288400-173290800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:173288400-173291000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:173288400-173291800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:173288600-173290600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:173288600-173290800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr2:173289000-173291600	Weak transcription	Adipose Nuclei	Adipose
16	chr2:173289400-173291400	Weak transcription	NHEK	skin
17	chr2:173289600-173290800	Weak transcription	Thymus	Thymus
18	chr2:173290200-173290400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:173290200-173290400	Enhancers	Psoas Muscle	Psoas
20	chr2:173290200-173290600	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr2:173290200-173291400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr2:173290200-173291400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:173290200-173291600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr2:173290200-173291600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:173290200-173291600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr2:173290200-173291800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr2:173290200-173291800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:173290200-173292000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon

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